https://manual.genomeview.org/api.php?action=feedcontributions&user=69.173.108.246&feedformat=atomGenomeView Manual - User contributions [en]2024-03-29T00:24:16ZUser contributionsMediaWiki 1.35.6https://manual.genomeview.org/index.php?title=Preparing_genome_synteny&diff=12990Preparing genome synteny2014-01-09T16:22:04Z<p>69.173.108.246: Created page with "The file format is pretty basic: First line has to be: "gvheader:syntenic" , without the quotes The remainder of the file is organized in 8 columns with the first four giving..."</p>
<hr />
<div>The file format is pretty basic:<br />
First line has to be: "gvheader:syntenic" , without the quotes<br />
<br />
The remainder of the file is organized in 8 columns with the first four giving information about the reference and the last four about the informant.<br />
<br />
0,1,2,3 name,start,end,strand of reference<br />
4,5,6,7 name,start,end,strand of informant</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_and_loading_data&diff=12989Preparing and loading data2014-01-09T16:21:34Z<p>69.173.108.246: /* Recommended file formats */</p>
<hr />
<div><br />
{{TOC|align=right}}<br />
<br />
<br />
<br />
There are several easy ways to load up data into GenomeView. Before you load your data, you may want to make sure you're using a supported format from the list below. Generally, GenomeView will notify you if it doesn't understand your data.<br />
<br />
==Loading data ==<br />
You can load your data files ...<br />
* ... by selecting "work with my data" in the [[Genome Explorer]]<br />
* ... by dragging them onto GenomeView<br />
* ... by selecting the 'File' menu and then 'Load data...' ([http://genomeview.org/content/load-data tutorial])<br />
* ... by pressing CTRL+O<br />
* ... by specifying them as argument on the [[command-line use|command-line]]<br />
* ... by loading a [[session file]]<br />
<br />
<br />
You can load preloaded data ...<br />
* ... by selecting a genome from the [[Genome Explorer]]<br />
* ... following a link from a [[Integration|GenomeView enabled website]]<br />
<br />
==Data preparation recipe==<br />
<br />
# Match identifiers: GenomeView uses the identifiers to link different sources, so make sure that the identifiers match (case-sensitive).<br />
# Create indices for data files that need it (check table below)<br />
# Convert file formats to get desired visuals (check table below)<br />
# Load data (see above)<br />
<br />
'''Why index files?''' Indexing will create a look-up table for GenomeView to load data on-the-fly. This will will speed up browsing and loading speed, as well as significantly reduce the amount of memory you need. For some file formats we recommend you create indices, for other we do not. See the table below for more details and links to instructions.<br />
<br />
<br />
==Recommended file formats ==<br />
This is a list of file formats that are recommended for different data types. See the full list of data types in the section below.<br />
<br />
<br />
<br />
<table border=1><br />
<tr><th>Data type</th><th>Recommended file format</th><th>Instructions</th></tr><br />
<tr><td>Reference sequence</td><td>fasta</td><td>[[Preparing reference sequence]]</td></tr><br />
<tr><td>Annotation</td><td>GFF3</td><td>[[Preparing annotation]]</td></tr><br />
<tr><td>Read a alignments</td><td>BAM</td><td>[[Preparing read data]]</td></tr><br />
<tr><td>Variation</td><td>VCF</td><td>[[Preparing VCF data]]</td></tr><br />
<tr><td>Coverage summary - continuous values</td><td>TDF</td><td>[[Preparing value data]]</td></tr><br />
<tr><td>Whole genome alignments</td><td>MAF</td><td>[[Preparing whole genome alignments]]</td></tr><br />
<tr><td>Genome synteny</td><td>experimental</td><td>[[Preparing genome synteny]]</td></tr><br />
</table><br />
<br />
== Supported data formats ==<br />
<br />
=== Reference sequence ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<br />
<tr><th></th><th></th><th></th><th>unindexed***</th><th>indexed</th><th></th></tr><br />
<br />
<tr><td valign="top" rowspan=2>Reference sequence</td><td><b>fasta</b> <sup>ยค</sup></td><td>Recommended<br/>[[Index FASTA]]</td><td>50 Mb</td><td>unlimited</td><td>GenomeView will query the user create index for you if you don't have one and the file is very large.</td></tr><br />
<br />
<tr><td>embl, genbank</td><td>Not possible</td><td>50 Mb</td><td>--</td><td>EMBL and genbank are mixed file formats that can contain both annotation and reference sequence at the same time.</td></tr><br />
<br />
</table><br />
=== Annotation ===<br />
<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td valign="top" rowspan=4>Annotation</td><td><b>gff</b> <sup>&#164;</sup></td><td>Not recommended<br />
[[Index GFF]]</td><td>50 Mb</td><td>unlimited</td><td></td></tr><br />
<br />
<tr><td>embl, genbank</td><td>Not possible</td><td>50 Mb</td><td>--</td><td>EMBL and genbank are mixed file formats that can contain both annotation and reference sequence at the same time.</td></tr><br />
<br />
<tr><td>bed</td><td>Not recommended [[Index BED]]</td><td>50 Mb or less</td><td>unlimited</td><td>By default data from a bed file is added to the CDS track, if you want it in a different track, you have to add a line a the top of the file 'track name=Track_name'. No white-space is allowed in the track name.</td></tr><br />
<tr><td>ptt, tbl </td><td>Not possible</td><td>50 Mb or less</td><td>--</td><td>Other standard annotation formats GenomeView understands</td></tr><br />
<tr><td></td><td>various formats</td><td>Not possible</td><td>50 Mb or less</td><td>--</td><td>GenomeView can directly parse the output of the following programs: Blast, GeneMark, TransTermHP, FindPeaks, MaqSNP, tRNA-scan</td></tr><br />
</table><br />
<br />
=== Whole genome alignments ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td valign="top" rowspan=3>Multiple genome alignment</td><td><b>maf</b> <sup>&#164;</sup></td><td>Recommended</td><td>100 Mb</td><td>unlimited</td><td>GenomeView will prompt you to create a compressed maf file and index it for you, if you're trying to load an unindexed maf file.<br/>MAF is the recommended file format for whole genome alignemnt of large/complex genomes</td></tr><br />
<br />
<tr><td><b>multi-fasta</b> <sup>&#164;</sup></td><td>Not possible</td><td>100 Mb</td><td>--</td><td>Recommended for small/simple genomes with a near 1:1 relationship.</td></tr><br />
<br />
<tr><td>aln, ClustalW</td><td>Not possible</td><td>100 Mb</td><td>--</td></tr><br />
</table><br />
<br />
=== Read alignments ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td valign="top" rowspan=2>Sequence read alignment</td><td><b>bam</b> <sup>&#164;</sup><br>[[Preparing read data]]</td><td>Required</td><td>--</td><td>unlimited</td><td>GenomeView will prompt you if there is no index and will create one for you. GenomeView can not automatically sort BAM files.</td></tr><br />
<br />
<tr><td>MAQ, MapView, BroadSolexa</td><td>Not possible</td><td>100 Mb</td><td>--</td></tr><br />
</table><br />
<br />
=== Read coverage summary - continuous value data ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td valign="top" rowspan=4>Read coverage summary</td><td><b> [[tdf]]</b> <sup>&#164;</sup></td><td>Native</td><td>unlimited</td><td>unlimited</td><td>[[TDF]] files can be created with the [[bam2tdf]] tool that is available for [https://sourceforge.net/projects/genomeview/files/TDformat/ download.]</td></tr><br />
<br />
<tr><td>bigwig</td><td>Native</td><td>unlimited</td><td>unlimited</td><td>This format can be used for any wig file, not just read coverage</td></tr><br />
<br />
<tr><td>[[pileup]]</td><td>Required</td><td>--</td><td>unlimited</td><td>The pileup format becomes slow when you have extreme read depth (>5000 x coverage)</td></tr><br />
<br />
<tr><td>wig</td><td>Not possible</td><td>50 Mb</td><td>--</td><td>We strongly recommend to [[wig2tdf|convert your wig files to TDF]]. <br />
GenomeView can automatically convert wig files to TDF. Caveats: 'track' information should all be on a single line, 'browser' lines will be ignored as the are specific to the UCSC Genome Browser. WIG files need to be sorted by chromosome and by genomic coordinate within the chromosome. BedGraph as well as Wiggle_0 format is supported. For the wiggle_0 type, both variableStep and fixedStep should work.</td></tr><br />
</table><br />
<br />
=== Genome variation and diversity ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td>Genome variation</td><td><b> [[vcf]]</b> <sup>&#164;</sup></td><td>Not recommended</td><td>--</td><td>unlimited</td><td>It is recommended to run [[reducevcf]] on VCF prior to loading them, this will speed up the loading time significantly.</td></tr><br />
<br />
</table><br />
<br />
<br />
=== Allele diversity ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td>Allele diversity summary</td><td><b> [[pileup]]</b> <sup>&#164;</sup></td><td>Required</td><td>--</td><td>unlimited</td><td>The pileup format becomes slow when you have extreme read depth (>5000 x coverage)</td></tr><br />
<br />
</table><br />
* Indicates whether this file format can/should be indexed. <br/><br />
** Recommended maximum file size. First value is without index, the second with index. This values are only guidelines. When loading multiple data sets, you should add the sizes.<br/><br />
*** Unindexed data files can be gzip compressed.<br />
<br />
<sup>&#164;</sup> Recommended file format for this data type.<br />
<br />
<br />
<br />
<br />
<h2>Output formats</h2><br />
(Modified) annotations can be saved as either GFF or EMBL.<br />
<br />
All data that is loaded can be exported in their original format. This will not include modifications.<br />
<br />
<h2>Converting formats</h2><br />
<a href="http://genomeview.org/loki/">We offer a few tools to convert files between formats.</a><br />
<br />
== Previous documentation pages ==<br />
<br />
<br />
<br />
[http://genomeview.org/content/data-formats Supported data formats]<br />
[http://genomeview.org/content/preparing-fasta-files Fasta files]<br />
<br />
[http://genomeview.org/content/preparing-feature-files Feature files]<br />
<br />
[http://genomeview.org/content/preparing-short-read-alignments Read data]<br />
<br />
[http://genomeview.org/content/preparing-pileup Coverage plots]</div>69.173.108.246https://manual.genomeview.org/index.php?title=Bam2tdf&diff=12980Bam2tdf2013-11-25T20:25:58Z<p>69.173.108.246: </p>
<hr />
<div>BAM2TDF is a command-line tool that converts BAM files to TDF (coverage) files.<br />
<br />
You can download the latest version from the GenomeView nightly builds:<br />
<br />
http://genomeview.org/jenkins/bam2tdf-nightly/<br />
<br />
Instructions:<br />
<br />
~$ java -jar bam2tdf.jar [-m <minimumMappingQuality>] <location of your bam file><br />
<br />
<br />
bam2tdf calculates fragment coverage, not physical coverage<br />
<br />
Requirements:<br />
- Java 7+<br />
- BAM file needs to be sorted and indexed</div>69.173.108.246https://manual.genomeview.org/index.php?title=Configuration_options&diff=10122Configuration options2013-11-18T19:38:49Z<p>69.173.108.246: /* Configuring track order */</p>
<hr />
<div>These pages discuss how to configure a number of things using the configuration file.<br />
<br />
There are several places from where GenomeView tries to load configuration information. It will look in the specified order.<br />
<ul><br />
<li>Config files specified in the session file</li><br />
<li>Configuration supplied on the command line or start-up URLwith the --config option</li><br />
<li>Personal config file. This can be changed through the menu File -> Configuration.</li><br />
<li>Default configuration present within the release package</li><br />
</ul><br />
<br />
The default configuration file is [http://sourceforge.net/p/genomeview/genomeview-code/ci/master/tree/resources/conf/default.conf available from the code repository] and should be considered the primary source of information regarding configuration options. <br />
<br />
== Configuring track order ==<br />
To configure the order of tracks you can use the <code>track:weight:XXX</code> configuration option. This will give a weight to each track and heavier tracks will be placed lower on the screen.<br />
<br />
For annotation features you have give the type as XXX. You cannot use the file name method below. For example:<br />
<br />
track:weight:gene=1<br />
track:weight:mRNA=2<br />
track:weight:CDS=3<br />
<br />
For any other data type, you have to specify the file file name or URL where the data resides. You cannot use the method described above.<br />
<br />
Some examples for remote files:<br />
<br />
<nowiki>track:weight:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=100</nowiki><br />
<nowiki>track:weight:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=200</nowiki><br />
<br />
<br />
This will also work with local files:<br />
track:weight:W:\thomas\rnaseq.bam=400<br />
track:weight:W:\thomas\chipseq.bam=500<br />
<br />
<br />
Deciding which method to use depends on the type of data: annotation are by type, other data is by file name.<br />
<br />
== Configuring track visibility ==<br />
To configure the initial visibility of tracks you can use the <code>track:visible:XXX</code> configuration option. This will tell GenomeView whether the track is initially visible or hidden<br />
<br />
For annotation features you give the type as XXX. For example:<br />
<br />
track:visible:gene=true<br />
track:visible:mRNA=false<br />
track:visible:CDS=true<br />
<br />
<br />
For any other data type, you have to specify the file file name or URL where the data resides. <br />
<br />
Some examples:<br />
<nowiki>track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=true</nowiki><br />
<nowiki>track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=false</nowiki><br />
<br />
==Configuring track aliases==<br />
<br />
<br />
To change the name that appears next to each track to something that is more informative than the fully qualified path name, you can use the <code>track:alias:XXX=ALIAS</code> configuration option. This will tell GenomeView which name it should display<br />
<br />
For annotation features you give the type as XXX. For example:<br />
track:alias:gene=All the genes<br />
track:alias:mRNA=MRNA track<br />
track:alias:CDS=Coding sequence features<br />
<br />
<br />
For any other data type, you have to specify the file file name or URL where the data resides. <br />
<br />
Some examples:<br />
<nowiki>track:alias:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=Directional RNA-seq MCF 7</nowiki><br />
<nowiki>track:alias:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=Shorter (75) directional RNA-seq for MCF 10</nowiki><br />
<br />
<br />
Note: Track aliases are unrelated to aliases set up in the session file with the ALIAS command. You can make a track alias in a session file with the OPTION command:<br />
OPTION track:alias:gene=All the genes</div>69.173.108.246https://manual.genomeview.org/index.php?title=Session_files&diff=10121Session files2013-11-18T19:00:25Z<p>69.173.108.246: </p>
<hr />
<div>Session files allow you to organize a large number of data files and config options in a single file.<br />
<br />
<br />
An example session file:<br />
http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php<br />
<br />
You can use 'View source', or something similar, in your browser to see the actual file structure. It is a plain text file with on each line a file that needs to be loaded.<br />
<br />
==File structure ==<br />
<br />
===Header===<br />
Make sure the file starts with a line that contains the words 'GenomeView' and 'session'. These two words have to be on the first line!<br />
<br />
We recommend:<br />
##GenomeView session<br />
<br />
This header is used to detect the file format by GenomeView.<br />
<br />
=== Body ===<br />
<br />
The remainder of the file contains lines that have various instructions to load data, configure GenomeView or load plugins. The table below has an overview of all options.<br />
<br />
{|<br />
!Instruction*<br />
!Value<br />
|-<br />
|CONFIG<br />
|URL or local file path to the configuration file. This line should be the first in the session file, otherwise some data may not have the correct configuration file when initializing.<br />
|-<br />
|DATA** <br />
|URL or local file path for a data file. This file will be loaded. You do not need to specify the index, GenomeView will look for it in the same folder.<br />
|-<br />
|PREFIX <br />
|URL or local file path prefix. The value of this instructions will be prepended to any DATA, PLUGIN or CONFIG pairs that follow this instruction. A PREFIX values is only valid for subsequent DATA, PLUGIN and CONFIG pairs. This can to simplify loading many files from multiple locations. To reset the PREFIX, you can use an empty value. You can use multiple PREFIX instructions through-out the session, they will each be valid for the following DATA, PLUGIN and CONFIG instructions, until reset with an alternative value.<br />
|-<br />
|OPTION <br />
|Key=value definition of a single configuration option. This is suited to override a few config options as needed.<br />
|-<br />
|ALIAS [primary name]=[display name]. <br />
|Add an additional synonym for an Entry (chromosome). This can be useful if your data has different identifiers for the same sequence in different files. The primary name will be used to connect the data types. Multiple primary names can point to the display name, in that case you can use the aliases to connect multiple different IDs.<br />
|-<br />
|LOCATION<br />
|Set the visible location to the specified location. The location needs to be specified [entry]:[start position]-[end position].<br />
|-<br />
|PLUGIN <br />
|Allows you to request the user to automatically install a plugin. The plugin needs to be specified as a URL to the zip file. You can use relative names in conjunction with the PREFIX parameter<br />
|}<br />
<br />
** The legacy keywords C, U and F will continue to work.<br />
<br />
Each of the lines should be organized like this:<br />
instruction[tab, colon or space]value<br />
<br />
For example, all of these are valid ways to specify a file<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/MT_H37RV_V2.fasta<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/annotation.gff<br />
DATA:http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/operon.gff<br />
<br />
===Example session file===<br />
<br />
##GenomeView session -- DO NOT DELETE THIS LINE<br />
CONFIG http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/tbconfig.txt<br />
ALIAS MT_H37RV_V2=MyTBGenome<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/MT_H37RV_V2.fasta<br />
PREFIX http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/<br />
DATA annotation.gff<br />
DATA operon.gff<br />
DATA sRNA.gff<br />
DATA rRNA.gff<br />
PREFIX<br />
PLUGIN http://www.broadinstitute.org/software/genomeview/resources/save2pdf-1.1.zip<br />
<br />
== Starting a session with a launch URL ==<br />
<br />
Important: You should use the JNLP file we provide as it will integrate the parameters into the start-up parameters of the webstart application.<br />
<br />
The basic set-up to start GenomeView with a [[session file]] is<br />
<nowiki>http://genomeview.org/start/launch.jnlp?--session <URL to the session file></nowiki><br />
<br />
<br />
For example<br />
[http://genomeview.org/start/launch.jnlp?--session%20http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php]<br />
<br />
== Hiding the session URL ==<br />
Typically you don't even have to expose this URL and you can use a simple PHP script index.php that redirects to that location.<br />
For example:<br />
<nowiki>header("Location: http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php");</nowiki></div>69.173.108.246https://manual.genomeview.org/index.php?title=Integration&diff=10120Integration2013-11-18T18:57:21Z<p>69.173.108.246: /* Present your data through a Java Web Start session (recommended) */</p>
<hr />
<div>http://genomeview.org/content/integration<br />
<br />
<i>Other topics that may be of interest: <a href="/content/integrating-genomeview-editor">Integrating as editor</a> and <a href="/content/communicating-genomeview">Communicating with GenomeView</a></i><br />
<br />
This page tries to explain how to integrate GenomeView in your website with your data. You can either make it available through Java Webstart, or as an applet. Whenever possible we recommend using Java Web <br />
Start as it has better cross-platform and cross-browser support.<br />
<br />
==General considerations==<br />
To present your data in GenomeView optimally, there are a number of things you have to keep in mind.<br />
<br />
<br />
===Indexing===<br />
Please follow the recommendation in the [[recommended file formats]] page.<br />
<br />
You will want to <a href="/content/preparing-fasta-files">index your reference sequence</a> to reduce loading times.<br />
<br />
You may want to index annotation files, but this is not recommended unless they are over 10 Mb when compressed with gzip because you will loose structural information.<br />
<br />
<p>To load an indexed file, you point GenomeView to the main file and GenomeView will try to find the index by itself. <br />
<br />
<br />
===Compression===<br />
<p>GenomeView supports GZIP compression transparently on all non-indexed file formats, i.e. compression and indexing are mutually exclusive. However as part of the indexing process, many file formats will be compressed.<br />
<br />
<br />
<br />
<p><strong>Short read data</strong><br />
<p>Depending on what information you want to get out of the visualization, there are basically two ways to load short read data. The first one is the <a href="/content/short-read-track">Short Read Track</a> which will give you a detailed view with all individual reads. The second one is the <a href="/content/pile-track">Pile up track</a> which will give a more of a summary view/ coverage plot based on your sequence reads. <br />
<br />
<p><a href="/content/preparing-short-read-alignments">Instructions to prepare data for the short read track</a><br />
<br />
<p><a href="/content/preparing-pileup">Instructions to prepare data for the pile up track</a><br />
<br />
==Present your data through a Java Web Start link==<br />
The fastest and simplest way to get started and with integrating GenomeView with your data is by directly constructing a webstart link.<br />
<br />
The default launch URL is located at http://genomeview.org/start/launch.jnlp. If you require a specific version, there are stable URLs available from the [[supported versions]] page.<br />
<br />
The next step is constructing your URL to load sequence and features. Below a sample URL, which will load some sequence with annotation and some short reads. It will start with the [100000,200000] region visible.<br />
<br />
<nowiki>http://genomeview.org/start/launch.jnlp?--position 100000:200000 --url http://www.broadinstitute.org/software/genomeview/demo/c_elegans/IV.fasta http://www.broadinstitute.org/software/genomeview/demo/c_elegans/IV.gff.gz http://www.broadinstitute.org/software/genomeview/demo/c_elegans/uwgs-rw_L2_FC6218_3.CHROMOSOME_IV.sorted.bam.bai</nowiki><br />
<br />
Pasting this URL in your browser will start GenomeView with data from C. elegans loaded.<br />
<br />
[[Command line options]] to GenomeView can be added after the question mark after the installation URL.<br />
<br />
The formalized version of the integration URL looks like this:<br />
<br />
http://genomeview.org/start/launch.jnlp?[command line options for GenomeView separated with spaces]<br />
<br />
<br />
'''Important:''' You should use the JNLP file we provide as it will integrate the parameters into the start-up parameters of the webstart application.<br />
<br />
==Present your data through a Java Web Start session (recommended)==<br />
A [[session file]] is a text file that contains instructions for GenomeView on which data to load and how to configure itself. <br />
<br />
The basic set-up to start GenomeView with a [[session file]] is<br />
<nowiki>http://genomeview.org/start/launch.jnlp?--session <URL to the session file></nowiki><br />
<br />
<br />
For example<br />
[http://genomeview.org/start/launch.jnlp?--session%20http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php]<br />
<br />
==Embedding GenomeView as an applet==<br />
<div style="color:red">Support for the applet version of GenomeView is currently on hold due to ever changing Java support from the various browser and OS vendors. It is impossible to maintain any semblance of stability. All of the material below may or may not work.</div><br />
<br />
The key code that needs to be included in the body of your web page is:<br />
<br />
<pre><br />
&lt;script type=&quot;text/javascript&quot; src=&quot;http://www.java.com/js/deployJava.js&quot;&gt;&lt;/script&gt;<br />
&lt;script type=&quot;text/javascript&quot; src=&quot;http://genomeview.org/start/genomeview.js&quot;&gt;&lt;/script&gt;<br />
<br />
&lt;script type=&quot;text/javascript&quot;&gt;<br />
var gv_url = null;<br />
var gv_config = 'http://genomeview.org/jsdemo/democonfig.txt'; <br />
var gv_extra = null;<br />
var gv_location = null;<br />
startGV(gv_url,gv_location,gv_config,gv_extra,500,400);<br />
&lt;/script&gt;<br />
</pre><br />
<br />
<p>The <code>gv_url</code> can be used to pre-load a reference sequence. This file will be loaded first and only then will GenomeView proceed with loading additional data.<br />
<br />
<p>The configuration file you want to use, can be specified using the <code>gv_config</code> option.<br />
<br />
<p>All other data that you want to have loaded can be specified in a space separated list in <code>gv_extra</code>. These data sets will be loaded in parallel.<br />
<br />
<p>The location that will initially be visible, can be set by <code>gv_location</code>. The position is in the format &lt;entry&gt;:&lt;start position&gt;:&lt;end position&gt; The entry part is optional can be omitted in which case it becomes &lt;start position&gt;:&lt;end position&gt;<br />
<br />
<p><em>Note: we strongly recommend you use the genomeview.js we provide as that's the one we keep up to date with progressing releases.</em></div>69.173.108.246https://manual.genomeview.org/index.php?title=Integration&diff=10119Integration2013-11-18T18:43:48Z<p>69.173.108.246: /* Present your data through a Java Web Start link */</p>
<hr />
<div>http://genomeview.org/content/integration<br />
<br />
<i>Other topics that may be of interest: <a href="/content/integrating-genomeview-editor">Integrating as editor</a> and <a href="/content/communicating-genomeview">Communicating with GenomeView</a></i><br />
<br />
This page tries to explain how to integrate GenomeView in your website with your data. You can either make it available through Java Webstart, or as an applet. Whenever possible we recommend using Java Web <br />
Start as it has better cross-platform and cross-browser support.<br />
<br />
==General considerations==<br />
To present your data in GenomeView optimally, there are a number of things you have to keep in mind.<br />
<br />
<br />
===Indexing===<br />
Please follow the recommendation in the [[recommended file formats]] page.<br />
<br />
You will want to <a href="/content/preparing-fasta-files">index your reference sequence</a> to reduce loading times.<br />
<br />
You may want to index annotation files, but this is not recommended unless they are over 10 Mb when compressed with gzip because you will loose structural information.<br />
<br />
<p>To load an indexed file, you point GenomeView to the main file and GenomeView will try to find the index by itself. <br />
<br />
<br />
===Compression===<br />
<p>GenomeView supports GZIP compression transparently on all non-indexed file formats, i.e. compression and indexing are mutually exclusive. However as part of the indexing process, many file formats will be compressed.<br />
<br />
<br />
<br />
<p><strong>Short read data</strong><br />
<p>Depending on what information you want to get out of the visualization, there are basically two ways to load short read data. The first one is the <a href="/content/short-read-track">Short Read Track</a> which will give you a detailed view with all individual reads. The second one is the <a href="/content/pile-track">Pile up track</a> which will give a more of a summary view/ coverage plot based on your sequence reads. <br />
<br />
<p><a href="/content/preparing-short-read-alignments">Instructions to prepare data for the short read track</a><br />
<br />
<p><a href="/content/preparing-pileup">Instructions to prepare data for the pile up track</a><br />
<br />
==Present your data through a Java Web Start link==<br />
The fastest and simplest way to get started and with integrating GenomeView with your data is by directly constructing a webstart link.<br />
<br />
The default launch URL is located at http://genomeview.org/start/launch.jnlp. If you require a specific version, there are stable URLs available from the [[supported versions]] page.<br />
<br />
The next step is constructing your URL to load sequence and features. Below a sample URL, which will load some sequence with annotation and some short reads. It will start with the [100000,200000] region visible.<br />
<br />
<nowiki>http://genomeview.org/start/launch.jnlp?--position 100000:200000 --url http://www.broadinstitute.org/software/genomeview/demo/c_elegans/IV.fasta http://www.broadinstitute.org/software/genomeview/demo/c_elegans/IV.gff.gz http://www.broadinstitute.org/software/genomeview/demo/c_elegans/uwgs-rw_L2_FC6218_3.CHROMOSOME_IV.sorted.bam.bai</nowiki><br />
<br />
Pasting this URL in your browser will start GenomeView with data from C. elegans loaded.<br />
<br />
[[Command line options]] to GenomeView can be added after the question mark after the installation URL.<br />
<br />
The formalized version of the integration URL looks like this:<br />
<br />
http://genomeview.org/start/launch.jnlp?[command line options for GenomeView separated with spaces]<br />
<br />
<br />
'''Important:''' You should use the JNLP file we provide as it will integrate the parameters into the start-up parameters of the webstart application.<br />
<br />
==Present your data through a Java Web Start session (recommended)==<br />
A [[session file]] is a text file that contains instructions for GenomeView on which data to load and how to configure itself. <br />
<br />
The basic set-up to start GenomeView with a [[session file]] is<br />
http://genomeview.org/start/launch.jnlp?--session <URL to the session file><br />
<br />
<br />
For example<br />
[http://genomeview.org/start/launch.jnlp?--session%20http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php]<br />
<br />
<br />
<br />
<br />
<br />
==Embedding GenomeView as an applet==<br />
<div style="color:red">Support for the applet version of GenomeView is currently on hold due to ever changing Java support from the various browser and OS vendors. It is impossible to maintain any semblance of stability. All of the material below may or may not work.</div><br />
<br />
The key code that needs to be included in the body of your web page is:<br />
<br />
<pre><br />
&lt;script type=&quot;text/javascript&quot; src=&quot;http://www.java.com/js/deployJava.js&quot;&gt;&lt;/script&gt;<br />
&lt;script type=&quot;text/javascript&quot; src=&quot;http://genomeview.org/start/genomeview.js&quot;&gt;&lt;/script&gt;<br />
<br />
&lt;script type=&quot;text/javascript&quot;&gt;<br />
var gv_url = null;<br />
var gv_config = 'http://genomeview.org/jsdemo/democonfig.txt'; <br />
var gv_extra = null;<br />
var gv_location = null;<br />
startGV(gv_url,gv_location,gv_config,gv_extra,500,400);<br />
&lt;/script&gt;<br />
</pre><br />
<br />
<p>The <code>gv_url</code> can be used to pre-load a reference sequence. This file will be loaded first and only then will GenomeView proceed with loading additional data.<br />
<br />
<p>The configuration file you want to use, can be specified using the <code>gv_config</code> option.<br />
<br />
<p>All other data that you want to have loaded can be specified in a space separated list in <code>gv_extra</code>. These data sets will be loaded in parallel.<br />
<br />
<p>The location that will initially be visible, can be set by <code>gv_location</code>. The position is in the format &lt;entry&gt;:&lt;start position&gt;:&lt;end position&gt; The entry part is optional can be omitted in which case it becomes &lt;start position&gt;:&lt;end position&gt;<br />
<br />
<p><em>Note: we strongly recommend you use the genomeview.js we provide as that's the one we keep up to date with progressing releases.</em></div>69.173.108.246https://manual.genomeview.org/index.php?title=Command_line_options&diff=10118Command line options2013-11-18T18:42:30Z<p>69.173.108.246: </p>
<hr />
<div><strong>Installation</strong><br />
To use GenomeView on your local PC, you first have to [http://downloads.sourceforge.net/genomeview/ download a local copy]<br />
<br />
Extract the contents of the zip file to a directory where you want to install GenomeView.<br />
<br />
Add this directory to the CLASSPATH if you want GenomeView to be accessible from anywhere on your system. Alternatively you can always start from this directory or you can qualify the full path to the jar-file each time you start GenomeView.<br />
<br />
<strong>Use locally</strong><br />
You can start GenomeView by issuing the following command at the prompt<br />
java -Xmx900m -jar genomeview.jar<br />
<br />
<br />
<strong>Loading files on start-up</strong><br />
You can instruct GenomeView to load files when it starts. All file names and URLs that are specified will be loaded. There are a few options you can use. Files are loaded concurrently, unless the --file or --url switch is used.<br />
<br />
<br />
<br />
Some examples:<br />
<br />
java -Xmx900m -jar genomeview-669.jar --file seq.fasta<br />
<br />
This command will start GenomeView with seq.fasta loaded.<br />
<br />
java -Xmx900m -jar genomeview.jar --position 2000:3500 --file seq.fasta feat.embl pred.embl add.embl<br />
<br />
Will start GenomeView with all the specified files loaded, but seq.fasta will be loaded first and zoomed to the region 2000-3500.<br />
<br />
<br />
<br />
<br />
<br />
== Available options ==<br />
Options for use on the command line or with website integration.<br />
{| <br />
| --file &lt;file&gt;<br />
| Load this file first, all other files will be loaded concurrently after this files has finished<br />
|- <br />
| --url &lt;url&gt;<br />
| Load the data from this url first. After this has finished, all other files will be loaded concurrently<br />
|- <br />
| --session &lt;url or file &gt;<br />
| Load the session from this URL or file. This parameter will override all others.<br />
|- <br />
| --config &lt;file or url&gt;<br />
| Load extra configuration options from this file or URL. This configuration will override default and user configuration. See <a href="/content/configuration">configuration</a> for more details.<br />
|- <br />
| --position &lt;position&gt;<br />
| Zoom to the supplied position on start-up. You need to use this in conjunction with the --url or --file option. First that file or url will be loaded and then GenomeView will zoom to the supplied position. The position is in the format <code>&lt;entry&gt;:&lt;start position&gt;:&lt;end position&gt;</code> The entry part can be omitted in which case it becomes <code>&lt;start position&gt;:&lt;end position&gt; </code><br />
|- <br />
| <em>remaining arguments</em><br />
| Load all remaining files and URLs specified on the command line<br />
|}</div>69.173.108.246https://manual.genomeview.org/index.php?title=Command_line_options&diff=10117Command line options2013-11-18T18:40:29Z<p>69.173.108.246: </p>
<hr />
<div><strong>Installation</strong><br />
To use GenomeView on your local PC, you first have to <a href="http://downloads.sourceforge.net/genomeview/">download a local copy</a>.<br />
<br />
Extract the contents of the zip file to a directory where you want to install GenomeView.<br />
<br />
Add this directory to the CLASSPATH if you want GenomeView to be accessible from anywhere on your system. Alternatively you can always start from this directory or you can qualify the full path to the jar-file each time you start GenomeView.<br />
<br />
<strong>Use locally</strong><br />
You can start GenomeView by issuing the following command at the prompt<br />
<code>java -Xmx900m -jar genomeview-&lt;version&gt;.jar</code><br />
where &lt;version&gt; corresponds to the version number of the package you downloaded. At the time of writing this was 669 so you would type:<br />
<code>java -Xmx900m -jar genomeview-669.jar</code><br />
<br />
<strong>Loading files on start-up</strong><br />
You can instruct GenomeView to load files when it starts. All file names and URLs that are specified will be loaded. There are a few options you can use. Files are loaded concurrently, unless the --file or --url switch is used.<br />
<br />
See the <a href="/content/command-line-options">command line options page</a> for more details.<br />
<br />
Some examples:<br />
<code><br />
$>java -Xmx900m -jar genomeview-669.jar --file seq.fasta<br />
</code><br />
This command will start GenomeView with seq.fasta loaded.<br />
<br />
<code><br />
$>java -Xmx900m -jar genomeview-669.jar --position 2000:3500 --file seq.fasta feat.embl pred.embl add.embl<br />
</code><br />
Will start GenomeView with all the specified files loaded, but seq.fasta will be loaded first and zoomed to the region 2000-3500.<br />
<br />
<br />
<br />
<br />
<br />
== Available options ==<br />
Options for use on the command line or with website integration.<br />
{| <br />
| --file &lt;file&gt;<br />
| Load this file first, all other files will be loaded concurrently after this files has finished<br />
|- <br />
| --url &lt;url&gt;<br />
| Load the data from this url first. After this has finished, all other files will be loaded concurrently<br />
|- <br />
| --session &lt;url or file &gt;<br />
| Load the session from this URL or file. This parameter will override all others.<br />
|- <br />
| --config &lt;file or url&gt;<br />
| Load extra configuration options from this file or URL. This configuration will override default and user configuration. See <a href="/content/configuration">configuration</a> for more details.<br />
|- <br />
| --position &lt;position&gt;<br />
| Zoom to the supplied position on start-up. You need to use this in conjunction with the --url or --file option. First that file or url will be loaded and then GenomeView will zoom to the supplied position. The position is in the format <code>&lt;entry&gt;:&lt;start position&gt;:&lt;end position&gt;</code> The entry part can be omitted in which case it becomes <code>&lt;start position&gt;:&lt;end position&gt; </code><br />
|- <br />
| <em>remaining arguments</em><br />
| Load all remaining files and URLs specified on the command line<br />
|}</div>69.173.108.246https://manual.genomeview.org/index.php?title=Command-line_use&diff=10116Command-line use2013-11-18T18:39:26Z<p>69.173.108.246: Redirected page to Command line options</p>
<hr />
<div>#REDIRECT[[Command_line_options]]</div>69.173.108.246https://manual.genomeview.org/index.php?title=Command_line_options&diff=10115Command line options2013-11-18T18:38:55Z<p>69.173.108.246: Created page with "== Available options == Options for use on the command line or with website integration. {| | --file &lt;file&gt; | Load this file first, all other files will be loaded conc..."</p>
<hr />
<div>== Available options ==<br />
Options for use on the command line or with website integration.<br />
{| <br />
| --file &lt;file&gt;<br />
| Load this file first, all other files will be loaded concurrently after this files has finished<br />
|- <br />
| --url &lt;url&gt;<br />
| Load the data from this url first. After this has finished, all other files will be loaded concurrently<br />
|- <br />
| --session &lt;url or file &gt;<br />
| Load the session from this URL or file. This parameter will override all others.<br />
|- <br />
| --config &lt;file or url&gt;<br />
| Load extra configuration options from this file or URL. This configuration will override default and user configuration. See <a href="/content/configuration">configuration</a> for more details.<br />
|- <br />
| --position &lt;position&gt;<br />
| Zoom to the supplied position on start-up. You need to use this in conjunction with the --url or --file option. First that file or url will be loaded and then GenomeView will zoom to the supplied position. The position is in the format <code>&lt;entry&gt;:&lt;start position&gt;:&lt;end position&gt;</code> The entry part can be omitted in which case it becomes <code>&lt;start position&gt;:&lt;end position&gt; </code><br />
|- <br />
| <em>remaining arguments</em><br />
| Load all remaining files and URLs specified on the command line<br />
|}</div>69.173.108.246https://manual.genomeview.org/index.php?title=Template:Linear-gradient&diff=10114Template:Linear-gradient2013-11-18T18:26:57Z<p>69.173.108.246: Created page with "<includeonly>background-image: -moz-linear-gradient({{{1|}}}, {{{2|}}}); background-image: -ms-linear-gradient({{{1|}}}, {{{2|}}}); background-image: -o-linear-gradient({{{1|}..."</p>
<hr />
<div><includeonly>background-image: -moz-linear-gradient({{{1|}}}, {{{2|}}}); background-image: -ms-linear-gradient({{{1|}}}, {{{2|}}}); background-image: -o-linear-gradient({{{1|}}}, {{{2|}}}); background-image: -webkit-linear-gradient({{{1|}}}, {{{2|}}}); background-image: linear-gradient({{{1|}}}, {{{2|}}});</includeonly></div>69.173.108.246https://manual.genomeview.org/index.php?title=Template:Box-shadow&diff=10113Template:Box-shadow2013-11-18T18:26:41Z<p>69.173.108.246: Created page with "<includeonly>-moz-box-shadow: {{{1|4px}}} {{{2|4px}}} {{{3|4px}}} {{{4|#CCC}}}; -webkit-box-shadow: {{{1|4px}}} {{{2|4px}}} {{{3|4px}}} {{{4|#CCC}}}; box-shadow: {{{1|4px}}} {..."</p>
<hr />
<div><includeonly>-moz-box-shadow: {{{1|4px}}} {{{2|4px}}} {{{3|4px}}} {{{4|#CCC}}}; -webkit-box-shadow: {{{1|4px}}} {{{2|4px}}} {{{3|4px}}} {{{4|#CCC}}}; box-shadow: {{{1|4px}}} {{{2|4px}}} {{{3|4px}}} {{{4|#CCC}}};</includeonly></div>69.173.108.246https://manual.genomeview.org/index.php?title=Template:Border-radius&diff=10112Template:Border-radius2013-11-18T18:26:23Z<p>69.173.108.246: Created page with "<includeonly>-moz-border-radius: {{{1|8px}}}; -webkit-border-radius: {{{1|8px}}}; border-radius: {{{1|8px}}};</includeonly>"</p>
<hr />
<div><includeonly>-moz-border-radius: {{{1|8px}}}; -webkit-border-radius: {{{1|8px}}}; border-radius: {{{1|8px}}};</includeonly></div>69.173.108.246https://manual.genomeview.org/index.php?title=Template:!&diff=10111Template:!2013-11-18T18:26:00Z<p>69.173.108.246: Created page with "|"</p>
<hr />
<div>|</div>69.173.108.246https://manual.genomeview.org/index.php?title=Template:Unicode&diff=10110Template:Unicode2013-11-18T18:25:24Z<p>69.173.108.246: Created page with "<span class="Unicode">{{{1}}}</span>"</p>
<hr />
<div><span class="Unicode">{{{1}}}</span></div>69.173.108.246https://manual.genomeview.org/index.php?title=Template:Key_press/core&diff=10109Template:Key press/core2013-11-18T18:25:06Z<p>69.173.108.246: Created page with "<kbd class="keyboard-key nowrap" style="border: 1px solid #aaa; {{border-radius|2px}} {{box-shadow|1px|2px|2px|#ddd}} background-color: #f9f9f9; {{linear-gradient|top|#eee, #f..."</p>
<hr />
<div><kbd class="keyboard-key nowrap" style="border: 1px solid #aaa; {{border-radius|2px}} {{box-shadow|1px|2px|2px|#ddd}} background-color: #f9f9f9; {{linear-gradient|top|#eee, #f9f9f9, #eee}} padding: 1px 3px; font-family: inherit; font-size: 0.85em;">{{#switch:{{lc:{{{1}}}}}<br />
| caps lock = {{Unicode|โช}} Caps Lock<br />
| [[caps lock]] = {{Unicode|โช}} [[Caps Lock]]<br />
| shift = {{Unicode|โง}} Shift<br />
| [[shift key|shift]] = {{Unicode|โง}} [[Shift key|Shift]]<br />
| enter = {{Unicode|โต}} Enter<br />
| [[enter key|enter]] = {{Unicode|โต}} [[Enter key|Enter]]<br />
| cmd = {{Unicode|โ}} Cmd<br />
| [[cmd key|cmd]]<br />
| [[command key|cmd]] = {{Unicode|โ}} [[Command key|Cmd]]<br />
| command = {{Unicode|โ}} Command<br />
| [[cmd key|command]]<br />
| [[command key|command]] = {{Unicode|โ}} [[Command key|Command]]<br />
| opt = {{Unicode|โฅ}} Opt<br />
| [[opt key|opt]]<br />
| [[option key|opt]] = {{Unicode|โฅ}} [[Option key|Opt]]<br />
| option = {{Unicode|โฅ}} Option<br />
| [[option key]]<br />
| [[opt key|option]]<br />
| [[option key|option]] = {{Unicode|โฅ}} [[Option key|Option]]<br />
| tab = Tab {{Unicode|โน}}<br />
| [[tab key|tab]] = [[Tab key|Tab]] {{Unicode|โน}}<br />
| backspace = โ Backspace<br />
| [[backspace]] = โ [[Backspace]]<br />
| win = {{Unicode|โ}} Win<br />
| [[win key|win]]<br />
| [[windows key|win]] = {{Unicode|โ}} [[Windows key|Win]]<br />
| menu = {{Unicode|โฃ}} Menu<br />
| [[menu key|menu]] = {{Unicode|โฃ}} [[Menu key|Menu]]<br />
| up = โ<br />
| [[arrow keys|up]] = [[Arrow keys|โ]]<br />
| down = โ<br />
| [[arrow keys|down]] = [[Arrow keys|โ]]<br />
| left = โ<br />
| [[arrow keys|left]] = [[Arrow keys|โ]]<br />
| right = โ<br />
| [[arrow keys|right]] = [[Arrow keys|โ]]<br />
| * = <nowiki>*</nowiki><br />
| # = <nowiki>#</nowiki><br />
| [[#]] = [[Number sign|#]]<br />
| : = <nowiki>:</nowiki><br />
| [[:]] = [[Colon (punctuation)|:]]<br />
| [[|]] = [[Pipe symbol|{{!}}]]<br />
<br />
<!-- Left & right analog sticks --><br />
| l-up<br />
| l up = Lโ<br />
| l-down<br />
| l down = Lโ<br />
| l-left<br />
| l left = Lโ<br />
| l-right<br />
| l right = Lโ<br />
| l-ne<br />
| l ne = Lโ<br />
| l-se<br />
| l se = Lโ<br />
| l-nw<br />
| l nw = Lโ<br />
| l-sw<br />
| l sw = Lโ<br />
<br />
| r-up<br />
| r up = Rโ<br />
| r-down<br />
| r down = Rโ<br />
| r-left<br />
| r left = Rโ<br />
| r-right<br />
| r right = Rโ<br />
| r-ne<br />
| r ne = Rโ<br />
| r-se<br />
| r se = Rโ<br />
| r-nw<br />
| r nw = Rโ<br />
| r-sw<br />
| r sw = Rโ<br />
<br />
<!-- PlayStation --><br />
| ps x<br />
| ex = {{unicode|ร}}<br />
| ps c<br />
| circle = {{unicode|โ}}<br />
| ps s<br />
| square = {{unicode|โก}}<br />
| ps t<br />
| triangle = {{unicode|โณ}}<br />
<br />
<!-- Nintendo 64 & GameCube --><br />
| c-up<br />
| c up = Cโ<br />
| c-down<br />
| c down = Cโ<br />
| c-left<br />
| c left = Cโ<br />
| c-right<br />
| c right = Cโ<br />
| c-ne<br />
| c ne = Cโ<br />
| c-se<br />
| c se = Cโ<br />
| c-nw<br />
| c nw = Cโ<br />
| c-sw<br />
| c sw = Cโ<br />
<br />
<!-- default --><br />
| #default = {{{1}}}<br />
}}</kbd></div>69.173.108.246https://manual.genomeview.org/index.php?title=Template:Key_press&diff=10108Template:Key press2013-11-18T18:24:51Z<p>69.173.108.246: Created page with "{{key press/core|{{{1}}}}}<!-- -->{{#if:{{{2|}}}|+{{key press/core|{{{2}}}}}}}<!-- -->{{#if:{{{3|}}}|+{{key press/core|{{{3}}}}}}}<!-- -->{{#if:{{{4|}}}|+{{key press/core|{{{4..."</p>
<hr />
<div>{{key press/core|{{{1}}}}}<!--<br />
-->{{#if:{{{2|}}}|+{{key press/core|{{{2}}}}}}}<!--<br />
-->{{#if:{{{3|}}}|+{{key press/core|{{{3}}}}}}}<!--<br />
-->{{#if:{{{4|}}}|+{{key press/core|{{{4}}}}}}}<!--<br />
-->{{#if:{{{5|}}}|+{{key press/core|{{{5}}}}}}}<!--<br />
-->{{#if:{{{6|}}}|[[Category:Wikipedia keypress template parameter needs fixing]]}}</div>69.173.108.246https://manual.genomeview.org/index.php?title=Navigation&diff=10107Navigation2013-11-18T18:24:18Z<p>69.173.108.246: </p>
<hr />
<div>=== Mouse ===<br />
{| class="wikitable" border="1"<br />
|-<br />
! Mouse/Key combo<br />
! Action<br />
|-<br />
| {{Key press|Ctrl|Scroll wheel}} or {{Key press|Alt|Scroll wheel}}<br />
| Zooming in or out<br />
|-<br />
| {{Key press|Scroll wheel }}<br />
| Move track view up or down<br />
|-<br />
| {{Key press|Shift|Scroll wheel}}<br />
| Move left or right<br />
|-<br />
| {{Key press|Mouse drag}}<br />
| Move left or right<br />
|-<br />
| {{Key press|Shift|Mouse drag}}<br />
| Select sequence (only in structure track)<br />
|}<br />
<br />
=== Keyboard ===<br />
{| class="wikitable" border="1"<br />
|-<br />
! Key combo<br />
! Action<br />
|-<br />
| {{Key press|Up}} or {{Key press|+}}<br />
| Zooming in<br />
|-<br />
| {{Key press|Down}} or {{Key press|-}}<br />
| Zoom out<br />
|-<br />
| {{Key press|Left}}<br />
| Move left<br />
|-<br />
| {{Key press|Right}}<br />
| Move right<br />
|}<br />
<br />
<br />
http://genomeview.org/content/navigation<br />
<br />
http://genomeview.org/content/keyboard-shortcuts<br />
<br />
http://genomeview.org/content/mouse-shortcuts</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_and_loading_data&diff=10106Preparing and loading data2013-11-18T18:04:49Z<p>69.173.108.246: </p>
<hr />
<div><br />
{{TOC|align=right}}<br />
<br />
<br />
<br />
There are several easy ways to load up data into GenomeView. Before you load your data, you may want to make sure you're using a supported format from the list below. Generally, GenomeView will notify you if it doesn't understand your data.<br />
<br />
==Loading data ==<br />
You can load your data files ...<br />
* ... by selecting "work with my data" in the [[Genome Explorer]]<br />
* ... by dragging them onto GenomeView<br />
* ... by selecting the 'File' menu and then 'Load data...' ([http://genomeview.org/content/load-data tutorial])<br />
* ... by pressing CTRL+O<br />
* ... by specifying them as argument on the [[command-line use|command-line]]<br />
* ... by loading a [[session file]]<br />
<br />
<br />
You can load preloaded data ...<br />
* ... by selecting a genome from the [[Genome Explorer]]<br />
* ... following a link from a [[Integration|GenomeView enabled website]]<br />
<br />
==Data preparation recipe==<br />
<br />
# Match identifiers: GenomeView uses the identifiers to link different sources, so make sure that the identifiers match (case-sensitive).<br />
# Create indices for data files that need it (check table below)<br />
# Convert file formats to get desired visuals (check table below)<br />
# Load data (see above)<br />
<br />
'''Why index files?''' Indexing will create a look-up table for GenomeView to load data on-the-fly. This will will speed up browsing and loading speed, as well as significantly reduce the amount of memory you need. For some file formats we recommend you create indices, for other we do not. See the table below for more details and links to instructions.<br />
<br />
<br />
==Recommended file formats ==<br />
This is a list of file formats that are recommended for different data types. See the full list of data types in the section below.<br />
<br />
<br />
<br />
<table border=1><br />
<tr><th>Data type</th><th>Recommended file format</th><th>Instructions</th></tr><br />
<tr><td>Reference sequence</td><td>fasta</td><td>[[Preparing reference sequence]]</td></tr><br />
<tr><td>Annotation</td><td>GFF3</td><td>[[Preparing annotation]]</td></tr><br />
<tr><td>Read a alignments</td><td>BAM</td><td>[[Preparing read data]]</td></tr><br />
<tr><td>Variation</td><td>VCF</td><td>[[Preparing VCF data]]</td></tr><br />
<tr><td>Coverage summary - continuous values</td><td>TDF</td><td>[[Preparing value data]]</td></tr><br />
<tr><td>Whole genome alignments</td><td>MAF</td><td>[[Preparing whole genome alignments]]</td></tr><br />
<br />
</table><br />
<br />
== Supported data formats ==<br />
<br />
=== Reference sequence ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<br />
<tr><th></th><th></th><th></th><th>unindexed***</th><th>indexed</th><th></th></tr><br />
<br />
<tr><td valign="top" rowspan=2>Reference sequence</td><td><b>fasta</b> <sup>ยค</sup></td><td>Recommended<br/>[[Index FASTA]]</td><td>50 Mb</td><td>unlimited</td><td>GenomeView will query the user create index for you if you don't have one and the file is very large.</td></tr><br />
<br />
<tr><td>embl, genbank</td><td>Not possible</td><td>50 Mb</td><td>--</td><td>EMBL and genbank are mixed file formats that can contain both annotation and reference sequence at the same time.</td></tr><br />
<br />
</table><br />
=== Annotation ===<br />
<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td valign="top" rowspan=4>Annotation</td><td><b>gff</b> <sup>&#164;</sup></td><td>Not recommended<br />
[[Index GFF]]</td><td>50 Mb</td><td>unlimited</td><td></td></tr><br />
<br />
<tr><td>embl, genbank</td><td>Not possible</td><td>50 Mb</td><td>--</td><td>EMBL and genbank are mixed file formats that can contain both annotation and reference sequence at the same time.</td></tr><br />
<br />
<tr><td>bed</td><td>Not recommended [[Index BED]]</td><td>50 Mb or less</td><td>unlimited</td><td>By default data from a bed file is added to the CDS track, if you want it in a different track, you have to add a line a the top of the file 'track name=Track_name'. No white-space is allowed in the track name.</td></tr><br />
<tr><td>ptt, tbl </td><td>Not possible</td><td>50 Mb or less</td><td>--</td><td>Other standard annotation formats GenomeView understands</td></tr><br />
<tr><td></td><td>various formats</td><td>Not possible</td><td>50 Mb or less</td><td>--</td><td>GenomeView can directly parse the output of the following programs: Blast, GeneMark, TransTermHP, FindPeaks, MaqSNP, tRNA-scan</td></tr><br />
</table><br />
<br />
=== Whole genome alignments ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td valign="top" rowspan=3>Multiple genome alignment</td><td><b>maf</b> <sup>&#164;</sup></td><td>Recommended</td><td>100 Mb</td><td>unlimited</td><td>GenomeView will prompt you to create a compressed maf file and index it for you, if you're trying to load an unindexed maf file.<br/>MAF is the recommended file format for whole genome alignemnt of large/complex genomes</td></tr><br />
<br />
<tr><td><b>multi-fasta</b> <sup>&#164;</sup></td><td>Not possible</td><td>100 Mb</td><td>--</td><td>Recommended for small/simple genomes with a near 1:1 relationship.</td></tr><br />
<br />
<tr><td>aln, ClustalW</td><td>Not possible</td><td>100 Mb</td><td>--</td></tr><br />
</table><br />
<br />
=== Read alignments ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td valign="top" rowspan=2>Sequence read alignment</td><td><b>bam</b> <sup>&#164;</sup><br>[[Preparing read data]]</td><td>Required</td><td>--</td><td>unlimited</td><td>GenomeView will prompt you if there is no index and will create one for you. GenomeView can not automatically sort BAM files.</td></tr><br />
<br />
<tr><td>MAQ, MapView, BroadSolexa</td><td>Not possible</td><td>100 Mb</td><td>--</td></tr><br />
</table><br />
<br />
=== Read coverage summary - continuous value data ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td valign="top" rowspan=4>Read coverage summary</td><td><b> [[tdf]]</b> <sup>&#164;</sup></td><td>Native</td><td>unlimited</td><td>unlimited</td><td>[[TDF]] files can be created with the [[bam2tdf]] tool that is available for [https://sourceforge.net/projects/genomeview/files/TDformat/ download.]</td></tr><br />
<br />
<tr><td>bigwig</td><td>Native</td><td>unlimited</td><td>unlimited</td><td>This format can be used for any wig file, not just read coverage</td></tr><br />
<br />
<tr><td>[[pileup]]</td><td>Required</td><td>--</td><td>unlimited</td><td>The pileup format becomes slow when you have extreme read depth (>5000 x coverage)</td></tr><br />
<br />
<tr><td>wig</td><td>Not possible</td><td>50 Mb</td><td>--</td><td>We strongly recommend to [[wig2tdf|convert your wig files to TDF]]. <br />
GenomeView can automatically convert wig files to TDF. Caveats: 'track' information should all be on a single line, 'browser' lines will be ignored as the are specific to the UCSC Genome Browser. WIG files need to be sorted by chromosome and by genomic coordinate within the chromosome. BedGraph as well as Wiggle_0 format is supported. For the wiggle_0 type, both variableStep and fixedStep should work.</td></tr><br />
</table><br />
<br />
=== Genome variation and diversity ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td>Genome variation</td><td><b> [[vcf]]</b> <sup>&#164;</sup></td><td>Not recommended</td><td>--</td><td>unlimited</td><td>It is recommended to run [[reducevcf]] on VCF prior to loading them, this will speed up the loading time significantly.</td></tr><br />
<br />
</table><br />
<br />
<br />
=== Allele diversity ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td>Allele diversity summary</td><td><b> [[pileup]]</b> <sup>&#164;</sup></td><td>Required</td><td>--</td><td>unlimited</td><td>The pileup format becomes slow when you have extreme read depth (>5000 x coverage)</td></tr><br />
<br />
</table><br />
* Indicates whether this file format can/should be indexed. <br/><br />
** Recommended maximum file size. First value is without index, the second with index. This values are only guidelines. When loading multiple data sets, you should add the sizes.<br/><br />
*** Unindexed data files can be gzip compressed.<br />
<br />
<sup>&#164;</sup> Recommended file format for this data type.<br />
<br />
<br />
<br />
<br />
<h2>Output formats</h2><br />
(Modified) annotations can be saved as either GFF or EMBL.<br />
<br />
All data that is loaded can be exported in their original format. This will not include modifications.<br />
<br />
<h2>Converting formats</h2><br />
<a href="http://genomeview.org/loki/">We offer a few tools to convert files between formats.</a><br />
<br />
== Previous documentation pages ==<br />
<br />
<br />
<br />
[http://genomeview.org/content/data-formats Supported data formats]<br />
[http://genomeview.org/content/preparing-fasta-files Fasta files]<br />
<br />
[http://genomeview.org/content/preparing-feature-files Feature files]<br />
<br />
[http://genomeview.org/content/preparing-short-read-alignments Read data]<br />
<br />
[http://genomeview.org/content/preparing-pileup Coverage plots]</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_and_loading_data&diff=10105Preparing and loading data2013-11-18T18:04:34Z<p>69.173.108.246: /* Loading data */</p>
<hr />
<div><br />
{{TOC|align=right}}<br />
<br />
<br />
<br />
There are several easy ways to load up data into GenomeView. Before you load your data, you may want to make sure you're using a supported format from the list below. Generally, GenomeView will notify you if it doesn't understand your data.<br />
<br />
==Loading data ==<br />
You can load your data files ...<br />
* ... by selecting "work with my data" in the [[Genome Explorer]]<br />
* ... by dragging them onto GenomeView<br />
* ... by selecting the 'File' menu and then 'Load data...' ([http://genomeview.org/content/load-data tutorial])<br />
* ... by pressing CTRL+O<br />
* ... by specifying them as argument on the [[command-line use|command-line]]<br />
* ... by loading a [[session file]]<br />
<br />
<br />
You can load preloaded data ...<br />
* ... by selecting a genome from the [[Genome Explorer]]<br />
* ... following a link from a GenomeView enabled [[Integration|website]]<br />
<br />
==Data preparation recipe==<br />
<br />
# Match identifiers: GenomeView uses the identifiers to link different sources, so make sure that the identifiers match (case-sensitive).<br />
# Create indices for data files that need it (check table below)<br />
# Convert file formats to get desired visuals (check table below)<br />
# Load data (see above)<br />
<br />
'''Why index files?''' Indexing will create a look-up table for GenomeView to load data on-the-fly. This will will speed up browsing and loading speed, as well as significantly reduce the amount of memory you need. For some file formats we recommend you create indices, for other we do not. See the table below for more details and links to instructions.<br />
<br />
<br />
==Recommended file formats ==<br />
This is a list of file formats that are recommended for different data types. See the full list of data types in the section below.<br />
<br />
<br />
<br />
<table border=1><br />
<tr><th>Data type</th><th>Recommended file format</th><th>Instructions</th></tr><br />
<tr><td>Reference sequence</td><td>fasta</td><td>[[Preparing reference sequence]]</td></tr><br />
<tr><td>Annotation</td><td>GFF3</td><td>[[Preparing annotation]]</td></tr><br />
<tr><td>Read a alignments</td><td>BAM</td><td>[[Preparing read data]]</td></tr><br />
<tr><td>Variation</td><td>VCF</td><td>[[Preparing VCF data]]</td></tr><br />
<tr><td>Coverage summary - continuous values</td><td>TDF</td><td>[[Preparing value data]]</td></tr><br />
<tr><td>Whole genome alignments</td><td>MAF</td><td>[[Preparing whole genome alignments]]</td></tr><br />
<br />
</table><br />
<br />
== Supported data formats ==<br />
<br />
=== Reference sequence ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<br />
<tr><th></th><th></th><th></th><th>unindexed***</th><th>indexed</th><th></th></tr><br />
<br />
<tr><td valign="top" rowspan=2>Reference sequence</td><td><b>fasta</b> <sup>ยค</sup></td><td>Recommended<br/>[[Index FASTA]]</td><td>50 Mb</td><td>unlimited</td><td>GenomeView will query the user create index for you if you don't have one and the file is very large.</td></tr><br />
<br />
<tr><td>embl, genbank</td><td>Not possible</td><td>50 Mb</td><td>--</td><td>EMBL and genbank are mixed file formats that can contain both annotation and reference sequence at the same time.</td></tr><br />
<br />
</table><br />
=== Annotation ===<br />
<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td valign="top" rowspan=4>Annotation</td><td><b>gff</b> <sup>&#164;</sup></td><td>Not recommended<br />
[[Index GFF]]</td><td>50 Mb</td><td>unlimited</td><td></td></tr><br />
<br />
<tr><td>embl, genbank</td><td>Not possible</td><td>50 Mb</td><td>--</td><td>EMBL and genbank are mixed file formats that can contain both annotation and reference sequence at the same time.</td></tr><br />
<br />
<tr><td>bed</td><td>Not recommended [[Index BED]]</td><td>50 Mb or less</td><td>unlimited</td><td>By default data from a bed file is added to the CDS track, if you want it in a different track, you have to add a line a the top of the file 'track name=Track_name'. No white-space is allowed in the track name.</td></tr><br />
<tr><td>ptt, tbl </td><td>Not possible</td><td>50 Mb or less</td><td>--</td><td>Other standard annotation formats GenomeView understands</td></tr><br />
<tr><td></td><td>various formats</td><td>Not possible</td><td>50 Mb or less</td><td>--</td><td>GenomeView can directly parse the output of the following programs: Blast, GeneMark, TransTermHP, FindPeaks, MaqSNP, tRNA-scan</td></tr><br />
</table><br />
<br />
=== Whole genome alignments ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td valign="top" rowspan=3>Multiple genome alignment</td><td><b>maf</b> <sup>&#164;</sup></td><td>Recommended</td><td>100 Mb</td><td>unlimited</td><td>GenomeView will prompt you to create a compressed maf file and index it for you, if you're trying to load an unindexed maf file.<br/>MAF is the recommended file format for whole genome alignemnt of large/complex genomes</td></tr><br />
<br />
<tr><td><b>multi-fasta</b> <sup>&#164;</sup></td><td>Not possible</td><td>100 Mb</td><td>--</td><td>Recommended for small/simple genomes with a near 1:1 relationship.</td></tr><br />
<br />
<tr><td>aln, ClustalW</td><td>Not possible</td><td>100 Mb</td><td>--</td></tr><br />
</table><br />
<br />
=== Read alignments ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td valign="top" rowspan=2>Sequence read alignment</td><td><b>bam</b> <sup>&#164;</sup><br>[[Preparing read data]]</td><td>Required</td><td>--</td><td>unlimited</td><td>GenomeView will prompt you if there is no index and will create one for you. GenomeView can not automatically sort BAM files.</td></tr><br />
<br />
<tr><td>MAQ, MapView, BroadSolexa</td><td>Not possible</td><td>100 Mb</td><td>--</td></tr><br />
</table><br />
<br />
=== Read coverage summary - continuous value data ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td valign="top" rowspan=4>Read coverage summary</td><td><b> [[tdf]]</b> <sup>&#164;</sup></td><td>Native</td><td>unlimited</td><td>unlimited</td><td>[[TDF]] files can be created with the [[bam2tdf]] tool that is available for [https://sourceforge.net/projects/genomeview/files/TDformat/ download.]</td></tr><br />
<br />
<tr><td>bigwig</td><td>Native</td><td>unlimited</td><td>unlimited</td><td>This format can be used for any wig file, not just read coverage</td></tr><br />
<br />
<tr><td>[[pileup]]</td><td>Required</td><td>--</td><td>unlimited</td><td>The pileup format becomes slow when you have extreme read depth (>5000 x coverage)</td></tr><br />
<br />
<tr><td>wig</td><td>Not possible</td><td>50 Mb</td><td>--</td><td>We strongly recommend to [[wig2tdf|convert your wig files to TDF]]. <br />
GenomeView can automatically convert wig files to TDF. Caveats: 'track' information should all be on a single line, 'browser' lines will be ignored as the are specific to the UCSC Genome Browser. WIG files need to be sorted by chromosome and by genomic coordinate within the chromosome. BedGraph as well as Wiggle_0 format is supported. For the wiggle_0 type, both variableStep and fixedStep should work.</td></tr><br />
</table><br />
<br />
=== Genome variation and diversity ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td>Genome variation</td><td><b> [[vcf]]</b> <sup>&#164;</sup></td><td>Not recommended</td><td>--</td><td>unlimited</td><td>It is recommended to run [[reducevcf]] on VCF prior to loading them, this will speed up the loading time significantly.</td></tr><br />
<br />
</table><br />
<br />
<br />
=== Allele diversity ===<br />
<table border=1><br />
<tr><th>Data type</th><th>File format</th><th>Index*</th><th colspan=2>Max size**</th><th>Comments</th></tr><br />
<tr><td>Allele diversity summary</td><td><b> [[pileup]]</b> <sup>&#164;</sup></td><td>Required</td><td>--</td><td>unlimited</td><td>The pileup format becomes slow when you have extreme read depth (>5000 x coverage)</td></tr><br />
<br />
</table><br />
* Indicates whether this file format can/should be indexed. <br/><br />
** Recommended maximum file size. First value is without index, the second with index. This values are only guidelines. When loading multiple data sets, you should add the sizes.<br/><br />
*** Unindexed data files can be gzip compressed.<br />
<br />
<sup>&#164;</sup> Recommended file format for this data type.<br />
<br />
<br />
<br />
<br />
<h2>Output formats</h2><br />
(Modified) annotations can be saved as either GFF or EMBL.<br />
<br />
All data that is loaded can be exported in their original format. This will not include modifications.<br />
<br />
<h2>Converting formats</h2><br />
<a href="http://genomeview.org/loki/">We offer a few tools to convert files between formats.</a><br />
<br />
== Previous documentation pages ==<br />
<br />
<br />
<br />
[http://genomeview.org/content/data-formats Supported data formats]<br />
[http://genomeview.org/content/preparing-fasta-files Fasta files]<br />
<br />
[http://genomeview.org/content/preparing-feature-files Feature files]<br />
<br />
[http://genomeview.org/content/preparing-short-read-alignments Read data]<br />
<br />
[http://genomeview.org/content/preparing-pileup Coverage plots]</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_reference_sequence&diff=10104Preparing reference sequence2013-11-18T18:01:39Z<p>69.173.108.246: </p>
<hr />
<div>To be able to easily handle large reference genomes, it is required that they are indexed. This can be done with the <em>faidx</em> command from the samtools package.<br />
<br />
If you are also preparing HTS data sets in the BAM format, this step will also be part of that procedure, so either you move right to the [[Preparing_read_data|short read preparation page]] or you can skip the step there whenever you're ready.<br />
<br />
To index a fasta file you run <br />
samtools faidx reference.fasta<br />
<br />
<br />
==Attention==<br />
If your file was called reference.fasta, GenomeView will search for reference.fasta.fai in the same directory. If you want to be able to load large files, make sure those two files are correctly named and in the same folder.<br />
<br />
You can [http://samtools.sourceforge.net download the samtools package from Sourceforge].</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_reference_sequence&diff=10103Preparing reference sequence2013-11-18T18:00:59Z<p>69.173.108.246: </p>
<hr />
<div>To be able to easily handle large reference genomes, it is required that they are indexed. This can be done with the <em>faidx</em> command from the samtools package.<br />
<br />
If you are also preparing HTS data sets in the BAM format, this step will also be part of that procedure, so either you move right to the [[BAM|short read preparation page]] or you can skip the step there whenever you're ready.<br />
<br />
To index a fasta file you run <br />
samtools faidx reference.fasta<br />
<br />
<br />
==Attention==<br />
If your file was called reference.fasta, GenomeView will search for reference.fasta.fai in the same directory. If you want to be able to load large files, make sure those two files are correctly named and in the same folder.<br />
<br />
You can <a href="http://samtools.sourceforge.net/">download the samtools package from Sourceforge</a>.</div>69.173.108.246https://manual.genomeview.org/index.php?title=TDF&diff=10102TDF2013-11-18T15:41:43Z<p>69.173.108.246: Redirected page to Preparing value data</p>
<hr />
<div>#REDIRECT[[Preparing value data]]</div>69.173.108.246https://manual.genomeview.org/index.php?title=Editing_annotations&diff=10098Editing annotations2013-11-18T14:42:10Z<p>69.173.108.246: Blanked the page</p>
<hr />
<div></div>69.173.108.246https://manual.genomeview.org/index.php?title=Editing_annotations&diff=10097Editing annotations2013-11-18T14:39:23Z<p>69.173.108.246: Created page with "http://genomeview.org/content/integrating-genomeview-editor"</p>
<hr />
<div>http://genomeview.org/content/integrating-genomeview-editor</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_whole_genome_alignments&diff=10096Preparing whole genome alignments2013-11-18T14:26:31Z<p>69.173.108.246: /* Loading .maf files into GenomeView */</p>
<hr />
<div>==Creating a multiple alignment ==<br />
<br />
* You can use an aligner such as TBA (Threaded Blockset Aligner). This can be downloaded from http://www.bx.psu.edu/miller_lab/<br />
* Instructions for using TBA are here: http://www.bx.psu.edu/miller_lab/dist/tba_howto.pdf<br />
* A phylogenetic tree is a required input.<br />
* Three are 3 steps required to run TBA:<br />
# Generate a series of pair-wise alignments to โseedโ the multiple alignment process. <pre>Example: all_bz - "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" blastz.specs >&all_bz.log</pre><br />
# Generate the multiple alignment <pre>Example: tba "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" *.*.maf tba.maf >&tba.log</pre><br />
# "project" the alignment onto a reference sequence. This will not make it a reference-based alignment; it just allows for visualization.<pre> Example: maf_project tba.maf chicken > tba_project_chicken.maf</pre><br />
<br />
==Loading .maf files into GenomeView==<br />
Once you have a .maf multiple alignment, projected onto a reference genome, you can load this into GenomeView.<br />
<br />
First, verify that all contig IDโs used in the .maf file match the contig IDโs used in your genome sequence and annotation files. Load the genome sequence, annotation, and .maf file with matching contig IDโs into Genomeview.<br />
<br />
In order to view comparative annotations, you need to follow these steps:<br />
* Enable comparative annotations:<br />
**Under โFileโ, select โConfiguationโ.<br />
**Select the tab for โComparative trackโ.<br />
**Make sure the box for โEnable comparative annotationsโ is checked.<br />
*Load in one annotation file for each genome in your multiple alignment (checking to make sure all contig IDโs match those used in the .maf file).<br />
* You should now see annotations for each genome in the multiple alignment.</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_whole_genome_alignments&diff=10095Preparing whole genome alignments2013-11-18T14:25:59Z<p>69.173.108.246: /* Loading .maf files into GenomeView */</p>
<hr />
<div>==Creating a multiple alignment ==<br />
<br />
* You can use an aligner such as TBA (Threaded Blockset Aligner). This can be downloaded from http://www.bx.psu.edu/miller_lab/<br />
* Instructions for using TBA are here: http://www.bx.psu.edu/miller_lab/dist/tba_howto.pdf<br />
* A phylogenetic tree is a required input.<br />
* Three are 3 steps required to run TBA:<br />
# Generate a series of pair-wise alignments to โseedโ the multiple alignment process. <pre>Example: all_bz - "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" blastz.specs >&all_bz.log</pre><br />
# Generate the multiple alignment <pre>Example: tba "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" *.*.maf tba.maf >&tba.log</pre><br />
# "project" the alignment onto a reference sequence. This will not make it a reference-based alignment; it just allows for visualization.<pre> Example: maf_project tba.maf chicken > tba_project_chicken.maf</pre><br />
<br />
==Loading .maf files into GenomeView==<br />
Once you have a .maf multiple alignment, projected onto a reference genome, you can load this into GenomeView.<br />
<br />
First, verify that all contig IDโs used in the .maf file match the contig IDโs used in your genome sequence and annotation files. Load the genome sequence, annotation, and .maf file with matching contig IDโs into Genomeview.<br />
<br />
In order to view comparative annotations, you need to follow these steps:<br />
* Enable comparative annotations: <pre>Under โFileโ, select โConfiguationโ.<br/>Select the tab for โComparative trackโ.<br/>Make sure the box for โEnable comparative annotationsโ is checked.</pre><br />
# Load in one annotation file for each genome in your multiple alignment (checking to make sure all contig IDโs match those used in the .maf file).<br />
# You should now see annotations for each genome in the multiple alignment.</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_whole_genome_alignments&diff=10094Preparing whole genome alignments2013-11-18T14:25:39Z<p>69.173.108.246: /* Loading .maf files into GenomeView */</p>
<hr />
<div>==Creating a multiple alignment ==<br />
<br />
* You can use an aligner such as TBA (Threaded Blockset Aligner). This can be downloaded from http://www.bx.psu.edu/miller_lab/<br />
* Instructions for using TBA are here: http://www.bx.psu.edu/miller_lab/dist/tba_howto.pdf<br />
* A phylogenetic tree is a required input.<br />
* Three are 3 steps required to run TBA:<br />
# Generate a series of pair-wise alignments to โseedโ the multiple alignment process. <pre>Example: all_bz - "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" blastz.specs >&all_bz.log</pre><br />
# Generate the multiple alignment <pre>Example: tba "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" *.*.maf tba.maf >&tba.log</pre><br />
# "project" the alignment onto a reference sequence. This will not make it a reference-based alignment; it just allows for visualization.<pre> Example: maf_project tba.maf chicken > tba_project_chicken.maf</pre><br />
<br />
==Loading .maf files into GenomeView==<br />
Once you have a .maf multiple alignment, projected onto a reference genome, you can load this into GenomeView.<br />
<br />
First, verify that all contig IDโs used in the .maf file match the contig IDโs used in your genome sequence and annotation files. Load the genome sequence, annotation, and .maf file with matching contig IDโs into Genomeview.<br />
<br />
In order to view comparative annotations, you need to follow these steps:<br />
* Enable comparative annotations: <pre>Under โFileโ, select โConfiguationโ.<br />
Select the tab for โComparative trackโ.<br />
Make sure the box for โEnable comparative annotationsโ is checked.<br />
</pre><br />
# Load in one annotation file for each genome in your multiple alignment (checking to make sure all contig IDโs match those used in the .maf file).<br />
# You should now see annotations for each genome in the multiple alignment.</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_whole_genome_alignments&diff=10093Preparing whole genome alignments2013-11-18T14:25:05Z<p>69.173.108.246: </p>
<hr />
<div>==Creating a multiple alignment ==<br />
<br />
* You can use an aligner such as TBA (Threaded Blockset Aligner). This can be downloaded from http://www.bx.psu.edu/miller_lab/<br />
* Instructions for using TBA are here: http://www.bx.psu.edu/miller_lab/dist/tba_howto.pdf<br />
* A phylogenetic tree is a required input.<br />
* Three are 3 steps required to run TBA:<br />
# Generate a series of pair-wise alignments to โseedโ the multiple alignment process. <pre>Example: all_bz - "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" blastz.specs >&all_bz.log</pre><br />
# Generate the multiple alignment <pre>Example: tba "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" *.*.maf tba.maf >&tba.log</pre><br />
# "project" the alignment onto a reference sequence. This will not make it a reference-based alignment; it just allows for visualization.<pre> Example: maf_project tba.maf chicken > tba_project_chicken.maf</pre><br />
<br />
==Loading .maf files into GenomeView==<br />
*Once you have a .maf multiple alignment, projected onto a reference genome, you can load this into GenomeView.<br />
*First, verify that all contig IDโs used in the .maf file match the contig IDโs used in your genome sequence and annotation files. Load the genome sequence, annotation, and .maf file with matching contig IDโs into Genomeview.<br />
*In order to view comparative annotations, you need to follow these steps:<br />
** Enable comparative annotations:<br />
Under โFileโ, select โConfiguationโ.<br />
Select the tab for โComparative trackโ.<br />
Make sure the box for โEnable comparative annotationsโ is checked.<br />
## Load in one annotation file for each genome in your multiple alignment (checking to make sure all contig IDโs match those used in the .maf file).<br />
## You should now see annotations for each genome in the multiple alignment.</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_whole_genome_alignments&diff=10092Preparing whole genome alignments2013-11-18T14:24:45Z<p>69.173.108.246: </p>
<hr />
<div>==Creating a multiple alignment ==<br />
<br />
* You can use an aligner such as TBA (Threaded Blockset Aligner). This can be downloaded from http://www.bx.psu.edu/miller_lab/<br />
* Instructions for using TBA are here: http://www.bx.psu.edu/miller_lab/dist/tba_howto.pdf<br />
* A phylogenetic tree is a required input.<br />
* Three are 3 steps required to run TBA:<br />
# Generate a series of pair-wise alignments to โseedโ the multiple alignment process. <br />
Example: all_bz - "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" blastz.specs >&all_bz.log<br />
# Generate the multiple alignment<br />
Example: tba "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" *.*.maf tba.maf >&tba.log<br />
# "project" the alignment onto a reference sequence. This will not make it a reference-based alignment; it just allows for visualization.<pre> Example: maf_project tba.maf chicken > tba_project_chicken.maf</pre><br />
<br />
==Loading .maf files into GenomeView==<br />
*Once you have a .maf multiple alignment, projected onto a reference genome, you can load this into GenomeView.<br />
*First, verify that all contig IDโs used in the .maf file match the contig IDโs used in your genome sequence and annotation files. Load the genome sequence, annotation, and .maf file with matching contig IDโs into Genomeview.<br />
*In order to view comparative annotations, you need to follow these steps:<br />
** Enable comparative annotations:<br />
Under โFileโ, select โConfiguationโ.<br />
Select the tab for โComparative trackโ.<br />
Make sure the box for โEnable comparative annotationsโ is checked.<br />
## Load in one annotation file for each genome in your multiple alignment (checking to make sure all contig IDโs match those used in the .maf file).<br />
## You should now see annotations for each genome in the multiple alignment.</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_whole_genome_alignments&diff=10091Preparing whole genome alignments2013-11-18T14:24:12Z<p>69.173.108.246: Created page with "==Creating a multiple alignment == * You can use an aligner such as TBA (Threaded Blockset Aligner). This can be downloaded from http://www.bx.psu.edu/miller_lab/ * Instruct..."</p>
<hr />
<div>==Creating a multiple alignment ==<br />
<br />
* You can use an aligner such as TBA (Threaded Blockset Aligner). This can be downloaded from http://www.bx.psu.edu/miller_lab/<br />
* Instructions for using TBA are here: http://www.bx.psu.edu/miller_lab/dist/tba_howto.pdf<br />
* A phylogenetic tree is a required input.<br />
* Three are 3 steps required to run TBA:<br />
## Generate a series of pair-wise alignments to โseedโ the multiple alignment process. <br />
Example: all_bz - "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" blastz.specs >&all_bz.log<br />
## Generate the multiple alignment<br />
Example: tba "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" *.*.maf tba.maf >&tba.log<br />
## "project" the alignment onto a reference sequence. This will not make it a reference-based alignment; it just allows for visualization.<br />
## Example: maf_project tba.maf chicken > tba_project_chicken.maf<br />
<br />
==Loading .maf files into GenomeView==<br />
*Once you have a .maf multiple alignment, projected onto a reference genome, you can load this into GenomeView.<br />
*First, verify that all contig IDโs used in the .maf file match the contig IDโs used in your genome sequence and annotation files. Load the genome sequence, annotation, and .maf file with matching contig IDโs into Genomeview.<br />
*In order to view comparative annotations, you need to follow these steps:<br />
** Enable comparative annotations:<br />
Under โFileโ, select โConfiguationโ.<br />
Select the tab for โComparative trackโ.<br />
Make sure the box for โEnable comparative annotationsโ is checked.<br />
## Load in one annotation file for each genome in your multiple alignment (checking to make sure all contig IDโs match those used in the .maf file).<br />
## You should now see annotations for each genome in the multiple alignment.</div>69.173.108.246https://manual.genomeview.org/index.php?title=Supported_versions&diff=10043Supported versions2013-11-15T20:12:07Z<p>69.173.108.246: </p>
<hr />
<div>Currently available versions:<br />
<br />
{| <br />
! Version<br />
! Webstart<br />
! Applet*<br />
! JavaScript embedding<br />
! EOL<br />
|- <br />
| [http://genomeview.org/start/gv2250.jnlp 2250 (stable)]<br />
| [[File:yes.png]]<br />
| [[File:no.png]]<br />
| [[File:yes.png]]<br />
| August 2014<br />
|- <br />
| <a href="/start/gv2170.jnlp">2170 (experimental)</a><br />
| [[File:no.png]]<br />
| [[File:no.png]]<br />
| [[File:no.png]]<br />
| --<br />
|- <br />
| <a href="/start/gv2144.jnlp">2144 </a><br />
| [[File:yes.png]]<br />
| [[File:no.png]]<br />
| [[File:yes.png]]<br />
| May 2014<br />
|- <br />
| <a href="/start/gv2126.jnlp">2126</a><br />
| [[File:yes.png]]<br />
| [[File:no.png]]<br />
| [[File:yes.png]]<br />
| February 2014<br />
|- <br />
| <a href="/start/gv2082.jnlp">2082 (experimental)</a><br />
| [[File:no.png]]<br />
| [[File:no.png]]<br />
| [[File:no.png]]<br />
| --<br />
|- <br />
| <a href="/start/gv2020.jnlp">2020 </a><br />
| [[File:yes.png]]<br />
| [[File:no.png]]<br />
| [[File:no.png]]<br />
| November 2013<br />
|- <br />
| <a href="/start/gv1983.jnlp">1983</a><br />
| [[File:no.png]]<br />
| [[File:no.png]]<br />
| [[File:no.png]]<br />
| Discontinued<br />
|- <br />
| <a href="/start/gv1939.jnlp">1939</a><br />
| [[File:no.png]]<br />
| [[File:no.png]]<br />
| [[File:no.png]]<br />
| Discontinued<br />
|- <br />
| <a href="/start/gv1912.jnlp">1912</a><br />
| [[File:no.png]]<br />
| [[File:no.png]]<br />
| [[File:no.png]]<br />
| Discontinued<br />
|}<br />
<br />
<table><br />
<tr><td>[[File:yes.png]]</td><td>Support offered on a best effort basis</td></tr><br />
<tr><td>[[File:no.png]]</td><td>Support offered on a low priority best effort basis</td></tr><br />
</table><br />
<br />
<br />
The developers of GenomeView offer a limited best-effort support for recent versions free of charge. Unfortunately, as this is a free product, we cannot guarantee anything. If you need a guaranteed service level agreement, <a href="mailto:thomas@genomeview.org">contact the project manager</a> and we will work out a solution.<br />
<br />
We intend to provide one year support for newly released versions.<br />
<br />
EOL: End of Life: After this data we cannot guarantee that this version will continue to run. Files may be archived from the server and so on.<br />
<br />
<br />
If you need continued support for a particular feature or version past its EOL, you should <a href="mailto:thomas@genomeview.org">contact the project manager</a> for more information. We can work together to find a solution.<br />
<br />
*Since March 2013, the support for the applet version has become a very low priority. There are too many platform/browser issues and we have too few resources to deal with all of them.</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_value_data&diff=10021Preparing value data2013-11-15T18:34:06Z<p>69.173.108.246: /* Creating TDF files */</p>
<hr />
<div>There are three formats supported for value/continuous data. The TDF format is by far the most appropriate and the other formats should be considered legacy support. <br />
<br />
TDF is a tiled binary data format which contains the value plot, as well as multiple resolution summaries which allows fast retrieval at any scale.<br />
<br />
This format is an alternative to wig and the bigwig formats and is typically used for data that has a value per chromosomal position, like for example coverage data.<br />
<br />
You can create TDF files directly from BAM files or from wig files.<br />
<br />
== Creating TDF files (recommended)==<br />
* [[bam2tdf]]: convert read alignment to coverage plot<br />
* [[wig2tdf]]: convert wig formatted data to tdf formatted data<br />
<br />
== SAMTools pileup (includes diversity information, i.e. SNP track) ==<br />
<em>Note: file name extension should contain .pileup</em><br />
The first step to be able to browse a pileup is to generate one from your BAM file.<br />
<br />
samtools pileup -f reference.fasta sorted.bam >sorted.pileup<br />
<br />
As you run this command, you'll see that the generated file can be huge, even for small BAM files.<br />
<br />
To be able to browse it in GenomeView, it needs to be indexed with tabix, a tool that is also available from the SAMtools web page.<br />
<br />
<br />
sort -k1,1 -k2,2n sorted.pileup | bgzip -c > compressed.pileup.bgz<br />
tabix -s 1 -b 2 -e 2 compressed.pileup.bgz<br />
<br />
<br />
<h2>Tab delimited pileup (extension should contain '.swig')</h2><br />
The file should be organized in four columns.<br />
The first column holds the identifier of the sequence, the second column contains the genomic position, the third column contains the number of reads on the forward strand, the final column contains the number of reads on the reverse strand.<br />
<ol><br />
<li>Identifier</li><br />
<li>Genomic position (one-based)</li><br />
<li># forward reads</li><br />
<li># reverse reads</li><br />
</ol><br />
<br />
Example:<br />
chr1 11 46 43<br />
chr1 12 47 50<br />
chr1 13 48 61<br />
chr1 14 53 79<br />
<br />
<em>Note that the white-space between the columns are tabs, one tab between each column</em>.<br />
<br />
Once you have such a file, you can again index it for faster access and shorter download times.<br />
<br />
sort -T . -k1,1 -k2,2n filename | bgzip -c > filename.bgz<br />
tabix -s 1 -b 2 -e 2 filename.bgz<br />
<br />
<br />
It is recommended that you convert this format to TDF with [[wig2tdf]].<br />
<br />
<a href="http://sourceforge.net/projects/samtools/files/samtools/">Download samtools</a><br />
<a href="https://sourceforge.net/projects/samtools/files/tabix/">Download tabix</a></div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_value_data&diff=10020Preparing value data2013-11-15T18:33:52Z<p>69.173.108.246: /* SAMTools pileup (includes diversity information, i.e. SNP track) */</p>
<hr />
<div>There are three formats supported for value/continuous data. The TDF format is by far the most appropriate and the other formats should be considered legacy support. <br />
<br />
TDF is a tiled binary data format which contains the value plot, as well as multiple resolution summaries which allows fast retrieval at any scale.<br />
<br />
This format is an alternative to wig and the bigwig formats and is typically used for data that has a value per chromosomal position, like for example coverage data.<br />
<br />
You can create TDF files directly from BAM files or from wig files.<br />
<br />
== Creating TDF files ==<br />
* [[bam2tdf]]: convert read alignment to coverage plot<br />
* [[wig2tdf]]: convert wig formatted data to tdf formatted data<br />
<br />
<br />
== SAMTools pileup (includes diversity information, i.e. SNP track) ==<br />
<em>Note: file name extension should contain .pileup</em><br />
The first step to be able to browse a pileup is to generate one from your BAM file.<br />
<br />
samtools pileup -f reference.fasta sorted.bam >sorted.pileup<br />
<br />
As you run this command, you'll see that the generated file can be huge, even for small BAM files.<br />
<br />
To be able to browse it in GenomeView, it needs to be indexed with tabix, a tool that is also available from the SAMtools web page.<br />
<br />
<br />
sort -k1,1 -k2,2n sorted.pileup | bgzip -c > compressed.pileup.bgz<br />
tabix -s 1 -b 2 -e 2 compressed.pileup.bgz<br />
<br />
<br />
<h2>Tab delimited pileup (extension should contain '.swig')</h2><br />
The file should be organized in four columns.<br />
The first column holds the identifier of the sequence, the second column contains the genomic position, the third column contains the number of reads on the forward strand, the final column contains the number of reads on the reverse strand.<br />
<ol><br />
<li>Identifier</li><br />
<li>Genomic position (one-based)</li><br />
<li># forward reads</li><br />
<li># reverse reads</li><br />
</ol><br />
<br />
Example:<br />
chr1 11 46 43<br />
chr1 12 47 50<br />
chr1 13 48 61<br />
chr1 14 53 79<br />
<br />
<em>Note that the white-space between the columns are tabs, one tab between each column</em>.<br />
<br />
Once you have such a file, you can again index it for faster access and shorter download times.<br />
<br />
sort -T . -k1,1 -k2,2n filename | bgzip -c > filename.bgz<br />
tabix -s 1 -b 2 -e 2 filename.bgz<br />
<br />
<br />
It is recommended that you convert this format to TDF with [[wig2tdf]].<br />
<br />
<a href="http://sourceforge.net/projects/samtools/files/samtools/">Download samtools</a><br />
<a href="https://sourceforge.net/projects/samtools/files/tabix/">Download tabix</a></div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_value_data&diff=10019Preparing value data2013-11-15T18:33:22Z<p>69.173.108.246: </p>
<hr />
<div>There are three formats supported for value/continuous data. The TDF format is by far the most appropriate and the other formats should be considered legacy support. <br />
<br />
TDF is a tiled binary data format which contains the value plot, as well as multiple resolution summaries which allows fast retrieval at any scale.<br />
<br />
This format is an alternative to wig and the bigwig formats and is typically used for data that has a value per chromosomal position, like for example coverage data.<br />
<br />
You can create TDF files directly from BAM files or from wig files.<br />
<br />
== Creating TDF files ==<br />
* [[bam2tdf]]: convert read alignment to coverage plot<br />
* [[wig2tdf]]: convert wig formatted data to tdf formatted data<br />
<br />
<br />
== SAMTools pileup (includes diversity information, i.e. SNP track) ==<br />
<em>Note: file name extension should contain .pileup</em><br />
The first step to be able to browse a pileup is to generate one from your BAM file.<br />
<code><br />
samtools pileup -f reference.fasta sorted.bam >sorted.pileup<br />
</code><br />
As you run this command, you'll see that the generated file can be huge, even for small BAM files.<br />
<br />
To be able to browse it in GenomeView, it needs to be indexed with tabix, a tool that is also available from the SAMtools web page.<br />
<br />
<code><br />
sort -k1,1 -k2,2n sorted.pileup | bgzip -c > compressed.pileup.bgz<br />
tabix -s 1 -b 2 -e 2 compressed.pileup.bgz<br />
</code><br />
<br />
<h2>Tab delimited pileup (extension should contain '.swig')</h2><br />
The file should be organized in four columns.<br />
The first column holds the identifier of the sequence, the second column contains the genomic position, the third column contains the number of reads on the forward strand, the final column contains the number of reads on the reverse strand.<br />
<ol><br />
<li>Identifier</li><br />
<li>Genomic position (one-based)</li><br />
<li># forward reads</li><br />
<li># reverse reads</li><br />
</ol><br />
<br />
Example:<br />
<code><br />
chr1 11 46 43<br />
chr1 12 47 50<br />
chr1 13 48 61<br />
chr1 14 53 79<br />
</code><br />
<em>Note that the white-space between the columns are tabs, one tab between each column</em>.<br />
<br />
Once you have such a file, you can again index it for faster access and shorter download times.<br />
<code><br />
sort -T . -k1,1 -k2,2n filename | bgzip -c > filename.bgz<br />
tabix -s 1 -b 2 -e 2 filename.bgz<br />
</code><br />
<br />
It is recommended that you convert this format to TDF with [[wig2tdf]].<br />
<br />
<a href="http://sourceforge.net/projects/samtools/files/samtools/">Download samtools</a><br />
<a href="https://sourceforge.net/projects/samtools/files/tabix/">Download tabix</a></div>69.173.108.246https://manual.genomeview.org/index.php?title=Bam2tdf&diff=10018Bam2tdf2013-11-15T18:32:02Z<p>69.173.108.246: </p>
<hr />
<div>BAM2TDF is a command-line tool that converts BAM files to TDF (coverage) files.<br />
<br />
You can download the latest version from the GenomeView nightly builds:<br />
<br />
http://genomeview.org/jenkins/bam2tdf-nightly/<br />
<br />
Instructions:<br />
<br />
~$ java -jar bam2tdf.jar <location of your bam file><br />
<br />
Requirements:<br />
- Java 7+<br />
- BAM file needs to be sorted and indexed</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_value_data&diff=10017Preparing value data2013-11-15T18:31:38Z<p>69.173.108.246: </p>
<hr />
<div>There are three formats supported for value/continuous data. The TDF format is by far the most appropriate and the other formats should be considered legacy support. <br />
<br />
TDF is a tiled binary data format which contains the value plot, as well as multiple resolution summaries which allows fast retrieval at any scale.<br />
<br />
This format is an alternative to wig and the bigwig formats and is typically used for data that has a value per chromosomal position, like for example coverage data.<br />
<br />
You can create TDF files directly from BAM files or from wig files.<br />
<br />
== Creating TDF files ==<br />
* [[bam2tdf]]: convert read alignment to coverage plot<br />
* [[wig2tdf]]: convert wig formatted data to tdf formatted data<br />
<br />
<br />
<br />
<a name="tdf"></a><h2>TDF coverage plot (recommended, coverage only)</h2><br />
<br />
<br />
<br />
<a name="pileup" ></a><h2>SAMTools pileup (includes diversity information, i.e. SNP track)</h2><br />
<em>Note: file name extension should contain .pileup</em><br />
The first step to be able to browse a pileup is to generate one from your BAM file.<br />
<code><br />
samtools pileup -f reference.fasta sorted.bam >sorted.pileup<br />
</code><br />
As you run this command, you'll see that the generated file can be huge, even for small BAM files.<br />
<br />
To be able to browse it in GenomeView, it needs to be indexed with tabix, a tool that is also available from the SAMtools web page.<br />
<br />
<code><br />
sort -k1,1 -k2,2n sorted.pileup | bgzip -c > compressed.pileup.bgz<br />
tabix -s 1 -b 2 -e 2 compressed.pileup.bgz<br />
</code><br />
<br />
<h2>Tab delimited pileup (extension should contain '.swig')</h2><br />
The file should be organized in four columns.<br />
The first column holds the identifier of the sequence, the second column contains the genomic position, the third column contains the number of reads on the forward strand, the final column contains the number of reads on the reverse strand.<br />
<ol><br />
<li>Identifier</li><br />
<li>Genomic position (one-based)</li><br />
<li># forward reads</li><br />
<li># reverse reads</li><br />
</ol><br />
<br />
Example:<br />
<code><br />
chr1 11 46 43<br />
chr1 12 47 50<br />
chr1 13 48 61<br />
chr1 14 53 79<br />
</code><br />
<em>Note that the white-space between the columns are tabs, one tab between each column</em>.<br />
<br />
Once you have such a file, you can again index it for faster access and shorter download times.<br />
<code><br />
sort -T . -k1,1 -k2,2n filename | bgzip -c > filename.bgz<br />
tabix -s 1 -b 2 -e 2 filename.bgz<br />
</code><br />
<br />
<h2>Resources</h2><br />
<a href="http://sourceforge.net/projects/samtools/files/samtools/">Download samtools</a><br />
<a href="https://sourceforge.net/projects/samtools/files/tabix/">Download tabix</a></div>69.173.108.246https://manual.genomeview.org/index.php?title=Unit_test_example_data_files&diff=10012Unit test example data files2013-10-25T14:30:09Z<p>69.173.108.246: /* (incomplete) List of data sets for testing */</p>
<hr />
<div>Data files to be used during Unit test should be uploaded to the file repository at SourceForge and should not be included in the code repository.<br />
<br />
There is a nifty utility class that will automatically retrieve data files from SF, you just need to give it the data set name.<br />
<br />
== (incomplete) List of data sets for testing ==<br />
{|<br />
!Identifier<br />
!Size<br />
!Description/Purpose<br />
|-<br />
|mini.fasta<br />
|<100 bytes<br />
|Very small fasta file to test the FASTA parser functions.<br />
|}</div>69.173.108.246https://manual.genomeview.org/index.php?title=Unit_test_example_data_files&diff=10011Unit test example data files2013-10-25T14:30:03Z<p>69.173.108.246: /* (incomplete) List of data sets for testing */</p>
<hr />
<div>Data files to be used during Unit test should be uploaded to the file repository at SourceForge and should not be included in the code repository.<br />
<br />
There is a nifty utility class that will automatically retrieve data files from SF, you just need to give it the data set name.<br />
<br />
== (incomplete) List of data sets for testing ==<br />
{|<br />
!Identifier<br />
!Size<br />
!Description/Purpose<br />
|-<br />
|mini.fasta<br />
|<100bytes<br />
|Very small fasta file to test the FASTA parser functions.<br />
|}</div>69.173.108.246https://manual.genomeview.org/index.php?title=Unit_test_example_data_files&diff=10010Unit test example data files2013-10-25T14:29:52Z<p>69.173.108.246: Created page with "Data files to be used during Unit test should be uploaded to the file repository at SourceForge and should not be included in the code repository. There is a nifty utility cl..."</p>
<hr />
<div>Data files to be used during Unit test should be uploaded to the file repository at SourceForge and should not be included in the code repository.<br />
<br />
There is a nifty utility class that will automatically retrieve data files from SF, you just need to give it the data set name.<br />
<br />
== (incomplete) List of data sets for testing ==<br />
{|<br />
!Identifier<br />
!Size<br />
!Description/Purpose<br />
|-<br />
|mini.fasta<br />
|<100bytes<br />
|Very small fasta file to test the FASTA parser functions.<br />
|)</div>69.173.108.246https://manual.genomeview.org/index.php?title=Main_Page&diff=10009Main Page2013-10-25T14:27:11Z<p>69.173.108.246: </p>
<hr />
<div>{{TOC|align=right}}<br />
<br />
Welcome to the GenomeView manual. These pages aim to answer any questions you may have as an end-user, a platform-user or as a contributing developer.<br />
<br />
This documentation is completely open for anyone to contribute to, just click the edit-button near the top and you can help make this a better resource for everyone.<br />
<br />
== [[Quick start|Getting started with GenomeView in 5 minutes]] ==<br />
<br />
<div style="float:left;width:49%"><br />
{{Box-header|title=User manual}}<br />
These manual pages describe how to use GenomeView and how to prepare your data to be usable in GenomeView.<br />
<br />
[[Starting GenomeView]]<br />
<br />
[[Preparing and loading data]] -- [[Preloaded data]]<br />
<br />
[[Navigation]] -- [[Keyboard short-cuts]]<br />
<br />
[[Visualizations]]<br />
<br />
[[Search for...]]<br />
<br />
[[Manipulating and configuring the views]]<br />
<br />
[[Editing annotations]]<br />
<br />
[[Exporting data and saving changes]]<br />
<br />
[[More functionality with plugins]]<br />
<br />
</div><br />
</div><br />
<br />
<div style="float:right;width:49%"><br />
{{Box-header|title=Getting help}}<br />
<br />
[[Frequently asked questions]]<br />
<br />
[[I have a problem, help me, please]]<br />
<br />
[[Report a bug or request a feature]]<br />
<br />
</div><br />
</div><br />
<br />
<br />
<br />
<div style="clear:both;"></div><br />
<br />
<br />
<div style="float:left;width:49%"><br />
{{Box-header|title=Platform-user manual}}<br />
These manual pages describe how to integrate GenomeView with your web-based platform or how to communicate with GenomeView from 3-rd party software. <br />
<br />
[[Using GenomeView from the command-line]]<br />
<br />
[[Integration]]<br />
<br />
[[Session files]] -- [[Configuration options]]<br />
<br />
[[Communicating with GenomeView]]<br />
<br />
[[Programming with GenomeView]]<br />
<br />
[[Setting up authentication and encryption]]<br />
<br />
[[Making a plugin]]<br />
<br />
[[Integrating GenomeView as an editor]]<br />
<br />
</div><br />
</div><br />
<br />
<div style="float:right;width:49%"><br />
{{Box-header|title=Developer manual}}<br />
These pages are aimed towards contributors to GenomeView and developers who work directly on the GenomeView code.<br />
<br />
Currently most of this documentation lives on [https://sourceforge.net/p/genomeview/wiki/ Sourceforge].<br />
<br />
[[Unit test example data files]]<br />
<br />
</div><br />
</div><br />
<div style="clear:both;"></div><br />
<br />
<br />
<br />
== Workshops, presentations and training ==</div>69.173.108.246https://manual.genomeview.org/index.php?title=Main_Page&diff=10008Main Page2013-10-25T14:26:54Z<p>69.173.108.246: </p>
<hr />
<div>{{TOC|align=right}}<br />
<br />
Welcome to the GenomeView manual. These pages aim to answer any questions you may have as an end-user, a platform-user or as a contributing developer.<br />
<br />
This documentation is completely open for anyone to contribute to, just click the edit-button near the top and you can help make this a better resource for everyone.<br />
<br />
== [[Quick start|Getting started with GenomeView in 5 minutes]] ==<br />
<br />
<div style="float:left;width:49%"><br />
{{Box-header|title=User manual}}<br />
These manual pages describe how to use GenomeView and how to prepare your data to be usable in GenomeView.<br />
<br />
[[Starting GenomeView]]<br />
<br />
[[Preparing and loading data]] -- [[Preloaded data]]<br />
<br />
[[Navigation]] -- [[Keyboard short-cuts]]<br />
<br />
[[Visualizations]]<br />
<br />
[[Search for...]]<br />
<br />
[[Manipulating and configuring the views]]<br />
<br />
[[Editing annotations]]<br />
<br />
[[Exporting data and saving changes]]<br />
<br />
[[More functionality with plugins]]<br />
<br />
</div><br />
</div><br />
<br />
<div style="float:right;width:49%"><br />
{{Box-header|title=Getting help}}<br />
<br />
[[Frequently asked questions]]<br />
<br />
[[I have a problem, help me, please]]<br />
<br />
[[Report a bug or request a feature]]<br />
<br />
</div><br />
</div><br />
<br />
<br />
<br />
<div style="clear:both;"></div><br />
<br />
<br />
<div style="float:left;width:49%"><br />
{{Box-header|title=Platform-user manual}}<br />
These manual pages describe how to integrate GenomeView with your web-based platform or how to communicate with GenomeView from 3-rd party software. <br />
<br />
[[Using GenomeView from the command-line]]<br />
<br />
[[Integration]]<br />
<br />
[[Session files]] -- [[Configuration options]]<br />
<br />
[[Communicating with GenomeView]]<br />
<br />
[[Programming with GenomeView]]<br />
<br />
[[Setting up authentication and encryption]]<br />
<br />
[[Making a plugin]]<br />
<br />
[[Integrating GenomeView as an editor]]<br />
<br />
</div><br />
</div><br />
<br />
<div style="float:right;width:49%"><br />
{{Box-header|title=Developer manual}}<br />
These pages are aimed towards contributors to GenomeView and developers who work directly on the GenomeView code.<br />
<br />
Currently most of this documentation lives on [https://sourceforge.net/p/genomeview/wiki/ Sourceforge].<br />
<br />
[[Unit test data files]]<br />
<br />
</div><br />
</div><br />
<div style="clear:both;"></div><br />
<br />
<br />
<br />
== Workshops, presentations and training ==</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_coverage_plots&diff=10007Preparing coverage plots2013-10-25T14:03:53Z<p>69.173.108.246: Redirected page to Preparing value data</p>
<hr />
<div>#REDIRECT[[Preparing_value_data]]</div>69.173.108.246https://manual.genomeview.org/index.php?title=Session_files&diff=10006Session files2013-10-25T13:33:06Z<p>69.173.108.246: </p>
<hr />
<div>Present your data through a Java Web Start session (recommended)<br />
<br />
Instead of putting all files in the URL as explained in the previous section, you can also point GenomeView to a so called session file which contains a list of files which need to be loaded.<br />
<br />
An example session file:<br />
http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php<br />
<br />
You can use 'View source', or something similar, in your browser to see the actual file structure. It is a plain text file with on each line a file that needs to be loaded.<br />
<br />
Make sure it starts with the line ##GenomeView session -- DO NOT...., as in the example. This header is used to detect the file format by GenomeView.<br />
<br />
You can add a C line at the top which would contain the link to the configuration file. It is important this line is the first one after the header.<br />
<br />
The U lines are links to data files, you can include as many as you want.<br />
<br />
The URL to start GenomeView with this sesssion would be:<br />
http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php<br />
<br />
Important: You should use the JNLP file we provide as it will integrate the parameters into the start-up parameters of the webstart application.<br />
<br />
Typically you don't even have to expose this URL and you can use an index.php that redirects to that location.<br />
header("Location: http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php");<br />
Session file format specification<br />
<br />
A session files consists out of 1 header line and 1 or more information lines.<br />
<br />
The header line should start with ##GenomeView session. This should be included literally (case-sensitive). The first line is the information GenomeView will use to detect the file format, in this case a session.<br />
<br />
The information lines consists of a letter key and the actual data. The different key letters are defined in the table below. The key and the data are separated with a single space, colon or tab.<br />
<br />
{|<br />
!Keyword*<br />
!Data<br />
|-<br />
|CONFIG<br />
|URL or local file path to the configuration file. This line should be the first in the session file, otherwise some data may not have the correct configuration file when initializing.<br />
|-<br />
|DATA** <br />
|URL or local file path for a data file. This file will be loaded. You do not need to specify the index, GenomeView will look for it in the same folder.<br />
|-<br />
|PREFIX <br />
|URL or local file path prefix. The value of this instructions will be prepended to any DATA or CONFIG pairs that follow this instruction. A PREFIX values is only valid for subsequent DATA and CONFIG pairs. This can to simplify loading many files from multiple locations. To reset the PREFIX, you can use an empty value.<br />
|-<br />
|OPTION <br />
|Key=value definition of a single configuration option. This is suited to override a few config options as needed.<br />
|-<br />
|ALIAS [primary name]=[alternative name]. <br />
|Add an additional synonym for an Entry (chromosome). This can be useful if your data has different identifiers for the same sequence in different files. The primary name will be used to connect the data types.<br />
|-<br />
|LOCATION<br />
|Set the visible location to the specified location. The location needs to be specified [entry]:[start position]-[end position].<br />
|-<br />
|PLUGIN <br />
|Allows you to request the user to automatically install a plugin. The plugin needs to be specified as a URL to the zip file. You can use relative names in conjunction with the PREFIX parameter<br />
|}<br />
<br />
** The legacy keywords C, U and F will continue to work.<br />
<br />
Example session file:<br />
<br />
##GenomeView session -- DO NOT DELETE THIS LINE<br />
CONFIG http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/tbconfig.txt<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/MT_H37RV_V2.fasta<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/annotation.gff<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/operon.gff<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/sRNA.gff<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/rRNA.gff</div>69.173.108.246https://manual.genomeview.org/index.php?title=Session_files&diff=10005Session files2013-10-25T13:32:20Z<p>69.173.108.246: </p>
<hr />
<div>Present your data through a Java Web Start session (recommended)<br />
<br />
Instead of putting all files in the URL as explained in the previous section, you can also point GenomeView to a so called session file which contains a list of files which need to be loaded.<br />
<br />
An example session file:<br />
http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php<br />
<br />
You can use 'View source', or something similar, in your browser to see the actual file structure. It is a plain text file with on each line a file that needs to be loaded.<br />
<br />
Make sure it starts with the line ##GenomeView session -- DO NOT...., as in the example. This header is used to detect the file format by GenomeView.<br />
<br />
You can add a C line at the top which would contain the link to the configuration file. It is important this line is the first one after the header.<br />
<br />
The U lines are links to data files, you can include as many as you want.<br />
<br />
The URL to start GenomeView with this sesssion would be:<br />
http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php<br />
<br />
Important: You should use the JNLP file we provide as it will integrate the parameters into the start-up parameters of the webstart application.<br />
<br />
Typically you don't even have to expose this URL and you can use an index.php that redirects to that location.<br />
header("Location: http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php");<br />
Session file format specification<br />
<br />
A session files consists out of 1 header line and 1 or more information lines.<br />
<br />
The header line should start with ##GenomeView session. This should be included literally (case-sensitive). The first line is the information GenomeView will use to detect the file format, in this case a session.<br />
<br />
The information lines consists of a letter key and the actual data. The different key letters are defined in the table below. The key and the data are separated with a single space, colon or tab.<br />
<br />
{|<br />
!Keyword*<br />
!Data<br />
|-<br />
|CONFIG<br />
|URL or local file path to the configuration file. This line should be the first in the session file, otherwise some data may not have the correct configuration file when initializing.<br />
|-<br />
|DATA** <br />
|URL or local file path for a data file. This file will be loaded. You do not need to specify the index, GenomeView will look for it in the same folder.<br />
|-<br />
|PREFIX <br />
|URL or local file path prefix. The value of this instructions will be prepended to any DATA or CONFIG pairs that follow this instruction. A PREFIX values is only valid for subsequent DATA and CONFIG pairs. This can to simplify loading many files from multiple locations. To reset the PREFIX, you can use an empty value.<br />
|-<br />
|OPTION <br />
|Key=value definition of a single configuration option. This is suited to override a few config options as needed.<br />
|-<br />
|ALIAS [primary name]=[alternative name]. <br />
|Add an additional synonym for an Entry (chromosome). This can be useful if your data has different identifiers for the same sequence in different files. The primary name will be used to connect the data types.<br />
|-<br />
|LOCATION<br />
|Set the visible location to the specified location. The location needs to be specified [entry]:[start position]-[end position].<br />
|-<br />
|PLUGIN <br />
|Allows you to request the user to automatically install a plugin. The plugin needs to be specified as a URL to the zip file. You can use relative names in conjunction with the PREFIX parameter<br />
|}<br />
<br />
* Must be upper-case<br />
** The legacy keywords C, U and F will continue to work.<br />
<br />
Example session file:<br />
<br />
##GenomeView session -- DO NOT DELETE THIS LINE<br />
CONFIG http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/tbconfig.txt<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/MT_H37RV_V2.fasta<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/annotation.gff<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/operon.gff<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/sRNA.gff<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/rRNA.gff</div>69.173.108.246https://manual.genomeview.org/index.php?title=Session_files&diff=10004Session files2013-10-25T13:18:47Z<p>69.173.108.246: Created page with "Present your data through a Java Web Start session (recommended) Instead of putting all files in the URL as explained in the previous section, you can also point GenomeView t..."</p>
<hr />
<div>Present your data through a Java Web Start session (recommended)<br />
<br />
Instead of putting all files in the URL as explained in the previous section, you can also point GenomeView to a so called session file which contains a list of files which need to be loaded.<br />
<br />
An example session file:<br />
http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php<br />
<br />
You can use 'View source', or something similar, in your browser to see the actual file structure. It is a plain text file with on each line a file that needs to be loaded.<br />
<br />
Make sure it starts with the line ##GenomeView session -- DO NOT...., as in the example. This header is used to detect the file format by GenomeView.<br />
<br />
You can add a C line at the top which would contain the link to the configuration file. It is important this line is the first one after the header.<br />
<br />
The U lines are links to data files, you can include as many as you want.<br />
<br />
The URL to start GenomeView with this sesssion would be:<br />
http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php<br />
<br />
Important: You should use the JNLP file we provide as it will integrate the parameters into the start-up parameters of the webstart application.<br />
<br />
Typically you don't even have to expose this URL and you can use an index.php that redirects to that location.<br />
header("Location: http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php");<br />
Session file format specification<br />
<br />
A session files consists out of 1 header line and 1 or more information lines.<br />
<br />
The header line should start with ##GenomeView session. This should be included literally (case-sensitive). The first line is the information GenomeView will use to detect the file format, in this case a session.<br />
<br />
The information lines consists of a letter key and the actual data. The different key letters are defined in the table below. The key and the data are separated with a single space, colon or tab.<br />
Keyword* Data<br />
CONFIG URL or local file path to the configuration file. This line should be the first in the session file, otherwise some data may not have the correct configuration file when initializing.<br />
DATA** URL or local file path for a data file. This file will be loaded. You do not need to specify the index, GenomeView will look for it in the same folder.<br />
PREFIX URL or local file path prefix. The value of this instructions will be prepended to any DATA or CONFIG pairs that follow this instruction. A PREFIX values is only valid for subsequent DATA and CONFIG pairs. This can to simplify loading many files from multiple locations. To reset the PREFIX, you can use an empty value.<br />
OPTION Key=value definition of a single configuration option. This is suited to override a few config options as needed.<br />
ALIAS [primary name]=[alternative name]. Add an additional synonym for an Entry (chromosome). This can be useful if your data has different identifiers for the same sequence in different files. The primary name will be used to connect the data types.<br />
LOCATION Set the visible location to the specified location. The location needs to be specified [entry]:[start position]-[end position].<br />
PLUGIN Allows you to request the user to automatically install a plugin. The plugin needs to be specified as a URL to the zip file. You can use relative names in conjunction with the PREFIX parameter<br />
* Must be upper-case<br />
** The legacy keywords C, U and F will continue to work.<br />
<br />
Example session file:<br />
<br />
##GenomeView session -- DO NOT DELETE THIS LINE<br />
CONFIG http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/tbconfig.txt<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/MT_H37RV_V2.fasta<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/annotation.gff<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/operon.gff<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/sRNA.gff<br />
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/rRNA.gff</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_read_data&diff=10002Preparing read data2013-10-24T15:30:17Z<p>69.173.108.246: </p>
<hr />
<div>{{TOC|align=right}}<br />
The best format to present short read alignments to GenomeView is the SAM/BAM format. You need to have your read data in this format and it has to be aligned to a reference genome.<br />
<br />
== Aligning reads ==<br />
GenomeView is a visualization tool and does not do the computationally intensive read alignment. There are however dozens of tools already available to do this job.<br />
<br />
If you need help aligning your reads, you may want to have a look at the [[Recipe to align reads]] to get some ideas.<br />
<br />
== Sorting and indexing ==<br />
Before you can visualize read data you need to prepare the data. This needs to be done because those files are generally huge and we do not want to read the complete file if we're only looking at a small portion of it.<br />
<br />
There are two things to prepare data fresh from the aligner.<br />
<br />
# Sort reads based on genomic coordinates<br />
# Index sorted reads.<br />
<br />
<br />
=== With Picard (OS independent, recommended) ===<br />
You need to have a a recent version of Java installed and you need to run these commands on the [[command-line]]. There are download links with each program where you can fetch the exact version that these manual pages were tested with. Alternatively, you may want to install a more recent version of [http://picard.sourceforge.net/ Picard].<br />
<br />
In this example we have a read alignment in BAM format called 'alignment.sam'. We use the program [http://picard.sourceforge.net/command-line-overview.shtml#SortSam SortSam] from Picard to sort the file by coordinates. This also works if your aligner gives you a BAM file as output, i.e. 'alignment.bam'<br />
<br />
'''Sorting'''<br />
The instruction below will sort the SAM file by coordinate.<br />
java -Xmx500m -jar SortSam.jar I=aligned.sam O=sorted.bam SO=coordinate<br />
[http://genomeview.org/loki/picard-tools-recent/SortSam.jar Download SortSam.jar]<br />
<br />
Important:<br />
# You may need to put the full path for SortSam.jar to the location where you installed the Picard programs. <br />
# You may need to put the full path to where the aligned.sam file sits and where you want the sorted.bam file to end up.<br />
# You have to make sure to replace 'alignment.sam' with the actual name of you aligned SAM/BAM file.<br />
# You have to make sure to replace 'sorted.bam' with the actual name that you want your sorted file to have.<br />
<br />
Sanity checks:<br />
# Make sure there are no errors reported on the console when running this instruction.<br />
# Make sure that you now have a file 'sorted.bam' and that it's not completely empty, i.e. it has a size > 0<br />
<br />
'''Indexing'''<br />
After you have sorted the file, you can index the resulting BAM file with the instruction below:<br />
<br />
java -Xmx500m -jar BuildBamIndex.jar I=sorted.bam<br />
[http://genomeview.org/loki/picard-tools-recent/BuildBamIndex.jar Download BuildBamIndex.jar]<br />
<br />
Important:<br />
# You may need to put the full path for BuildBamIndex.jar to the location where you installed the Picard programs. <br />
# You may need to put the full path to where the 'sorted.bam' file sits.<br />
<br />
<br />
Sanity checks:<br />
# Make sure there are no errors reported on the console when running this instruction.<br />
# Make sure that you now have a file 'sorted.bam.'''bai'''' and that it's not completely empty, i.e. it has a size > 0. This file will be created in the same directory as the 'sorted.bam' file.<br />
<br />
=== With SAMtools (Mac OS and Linux) ===<br />
Steps to get from the various aligner formats to the SAM format are available on the [http://samtools.sourceforge.net/ SAMtools website].<br />
<br />
You need to have SAMtools installed.<br />
<br />
Steps to go from SAM to indexed BAM.<br />
<br />
samtools faidx reference.fasta (will create reference.fasta.fai for the next step)<br />
<br />
samtools view -bS -t reference.fasta.fai alignment.sam -o alignment.bam<br />
<br />
samtools sort alignment.bam sorted (will create sorted.bam)<br />
<br />
samtools index sorted.bam (will create sorted.bam.bai, which is read by GenomeView together with the bam file)<br />
<br />
== Downsampling data ==<br />
Sometimes you don't want to look at all reads, but just at a fraction. This can be done by downsampling you BAM files before indexing.<br />
<br />
java -Xmx500m -jar DownsampleSam.jar I=sorted.bam O=downsample.bam P=0.1<br />
[http://genomeview.org/loki/picard-tools-recent/DownsampleSam.jar Download DownsampleSam.jar]<br />
<br />
<br />
<br />
The I parameter is the input file <br />
<br />
The O parameter is the output file <br />
<br />
The P parameter is the probability that a read is retained, so 0.1 means that 10% of the reads are kept.<br />
<br />
<br />
<br />
== Summary visualizations ==<br />
=== Coverage plots ===<br />
If you are primarily interested in the read coverage and not in individual reads, you may want to [[Preparing coverage plots|create coverage plots]].<br />
<br />
=== Variants ===<br />
If you are investigating SNPs or other genetic variants, you also may want to [[Recipe variant calls|create variant calls]].<br />
<br />
<br />
[[Category:User]][[Category:Platform]]</div>69.173.108.246https://manual.genomeview.org/index.php?title=Preparing_read_data&diff=10001Preparing read data2013-10-24T15:30:02Z<p>69.173.108.246: </p>
<hr />
<div>{{TOC|align=right}}<br />
The best format to present short read alignments to GenomeView is the SAM/BAM format. You need to have your read data in this format and it has to be aligned to a reference genome.<br />
<br />
== Aligning reads ==<br />
GenomeView is a visualization tool and does not do the computationally intensive read alignment. There are however dozens of tools already available to do this job.<br />
<br />
If you need help aligning your reads, you may want to have a look at the [[Recipe to align reads]] to get some ideas.<br />
<br />
== Sorting and indexing ==<br />
Before you can visualize read data you need to prepare the data. This needs to be done because those files are generally huge and we do not want to read the complete file if we're only looking at a small portion of it.<br />
<br />
There are two things to prepare data fresh from the aligner.<br />
<br />
# Sort reads based on genomic coordinates<br />
# Index sorted reads.<br />
<br />
<br />
=== With Picard (OS independent, recommended) ===<br />
You need to have a a recent version of Java installed and you need to run these commands on the [[command-line]]. There are download links with each program where you can fetch the exact version that these manual pages were tested with. Alternatively, you may want to install a more recent version of [http://picard.sourceforge.net/ Picard].<br />
<br />
In this example we have a read alignment in BAM format called 'alignment.sam'. We use the program [http://picard.sourceforge.net/command-line-overview.shtml#SortSam SortSam] from Picard to sort the file by coordinates. This also works if your aligner gives you a BAM file as output, i.e. 'alignment.bam'<br />
<br />
'''Sorting'''<br />
The instruction below will sort the SAM file by coordinate.<br />
java -Xmx500m -jar SortSam.jar I=aligned.sam O=sorted.bam SO=coordinate<br />
[http://genomeview.org/loki/picard-tools-recent/SortSam.jar Download SortSam.jar]<br />
<br />
Important:<br />
# You may need to put the full path for SortSam.jar to the location where you installed the Picard programs. <br />
# You may need to put the full path to where the aligned.sam file sits and where you want the sorted.bam file to end up.<br />
# You have to make sure to replace 'alignment.sam' with the actual name of you aligned SAM/BAM file.<br />
# You have to make sure to replace 'sorted.bam' with the actual name that you want your sorted file to have.<br />
<br />
Sanity checks:<br />
# Make sure there are no errors reported on the console when running this instruction.<br />
# Make sure that you now have a file 'sorted.bam' and that it's not completely empty, i.e. it has a size > 0<br />
<br />
'''Indexing'''<br />
After you have sorted the file, you can index the resulting BAM file with the instruction below:<br />
<br />
java -Xmx500m -jar BuildBamIndex.jar I=sorted.bam<br />
[http://genomeview.org/loki/picard-tools-recent/BuildBamIndex.jar Download BuildBamIndex.jar]<br />
<br />
Important:<br />
# You may need to put the full path for BuildBamIndex.jar to the location where you installed the Picard programs. <br />
# You may need to put the full path to where the 'sorted.bam' file sits.<br />
<br />
<br />
Sanity checks:<br />
# Make sure there are no errors reported on the console when running this instruction.<br />
# Make sure that you now have a file 'sorted.bam.'''bai'''' and that it's not completely empty, i.e. it has a size > 0. This file will be created in the same directory as the 'sorted.bam' file.<br />
<br />
=== With SAMtools (Mac OS and Linux) ===<br />
Steps to get from the various aligner formats to the SAM format are available on the [http://samtools.sourceforge.net/ SAMtools website].<br />
<br />
You need to have SAMtools installed.<br />
<br />
Steps to go from SAM to indexed BAM.<br />
<br />
samtools faidx reference.fasta (will create reference.fasta.fai for the next step)<br />
<br />
samtools view -bS -t reference.fasta.fai alignment.sam -o alignment.bam<br />
<br />
samtools sort alignment.bam sorted (will create sorted.bam)<br />
<br />
samtools index sorted.bam (will create sorted.bam.bai, which is read by GenomeView together with the bam file)<br />
<br />
== Downsampling data ==<br />
Some time you don't want to look at all reads, but just at a fraction. This can be done by downsampling you BAM files before indexing.<br />
<br />
java -Xmx500m -jar DownsampleSam.jar I=sorted.bam O=downsample.bam P=0.1<br />
[http://genomeview.org/loki/picard-tools-recent/DownsampleSam.jar Download DownsampleSam.jar]<br />
<br />
<br />
<br />
The I parameter is the input file <br />
<br />
The O parameter is the output file <br />
<br />
The P parameter is the probability that a read is retained, so 0.1 means that 10% of the reads are kept.<br />
<br />
<br />
<br />
== Summary visualizations ==<br />
=== Coverage plots ===<br />
If you are primarily interested in the read coverage and not in individual reads, you may want to [[Preparing coverage plots|create coverage plots]].<br />
<br />
=== Variants ===<br />
If you are investigating SNPs or other genetic variants, you also may want to [[Recipe variant calls|create variant calls]].<br />
<br />
<br />
[[Category:User]][[Category:Platform]]</div>69.173.108.246https://manual.genomeview.org/index.php?title=Main_Page&diff=10000Main Page2013-10-22T04:05:49Z<p>69.173.108.246: </p>
<hr />
<div>{{TOC|align=right}}<br />
<br />
Welcome to the GenomeView manual. These pages aim to answer any questions you may have as an end-user, a platform-user or as a contributing developer.<br />
<br />
This documentation is completely open for anyone to contribute to, just click the edit-button near the top and you can help make this a better resource for everyone.<br />
<br />
== [[Quick start|Getting started with GenomeView in 5 minutes]] ==<br />
<br />
<div style="float:left;width:49%"><br />
{{Box-header|title=User manual}}<br />
These manual pages describe how to use GenomeView and how to prepare your data to be usable in GenomeView.<br />
<br />
[[Starting GenomeView]]<br />
<br />
[[Preparing and loading data]] -- [[Preloaded data]]<br />
<br />
[[Navigation]] -- [[Keyboard short-cuts]]<br />
<br />
[[Visualizations]]<br />
<br />
[[Search for...]]<br />
<br />
[[Manipulating and configuring the views]]<br />
<br />
[[Editing annotations]]<br />
<br />
[[Exporting data and saving changes]]<br />
<br />
[[More functionality with plugins]]<br />
<br />
</div><br />
</div><br />
<br />
<div style="float:right;width:49%"><br />
{{Box-header|title=Getting help}}<br />
<br />
[[Frequently asked questions]]<br />
<br />
[[I have a problem, help me, please]]<br />
<br />
[[Report a bug or request a feature]]<br />
<br />
</div><br />
</div><br />
<br />
<br />
<br />
<div style="clear:both;"></div><br />
<br />
<br />
<div style="float:left;width:49%"><br />
{{Box-header|title=Platform-user manual}}<br />
These manual pages describe how to integrate GenomeView with your web-based platform or how to communicate with GenomeView from 3-rd party software. <br />
<br />
[[Using GenomeView from the command-line]]<br />
<br />
[[Integration]]<br />
<br />
[[Session files]] -- [[Configuration options]]<br />
<br />
[[Communicating with GenomeView]]<br />
<br />
[[Programming with GenomeView]]<br />
<br />
[[Setting up authentication and encryption]]<br />
<br />
[[Making a plugin]]<br />
<br />
[[Integrating GenomeView as an editor]]<br />
<br />
</div><br />
</div><br />
<br />
<div style="float:right;width:49%"><br />
{{Box-header|title=Developer manual}}<br />
These pages are aimed towards contributors to GenomeView and developers who work directly on the GenomeView code.<br />
<br />
Currently this documentation lives on [https://sourceforge.net/p/genomeview/wiki/ Sourceforge].<br />
<br />
</div><br />
</div><br />
<div style="clear:both;"></div><br />
<br />
<br />
<br />
== Workshops, presentations and training ==</div>69.173.108.246