Preparing whole genome alignments - Revision history

69.173.108.246: /* Loading .maf files into GenomeView */

2013-11-18T14:26:31Z

Loading .maf files into GenomeView

69.173.108.246: /* Loading .maf files into GenomeView */

2013-11-18T14:25:59Z

Loading .maf files into GenomeView

69.173.108.246: /* Loading .maf files into GenomeView */

2013-11-18T14:25:39Z

Loading .maf files into GenomeView

69.173.108.246 at 14:25, 18 November 2013

2013-11-18T14:25:05Z

69.173.108.246 at 14:24, 18 November 2013

2013-11-18T14:24:45Z

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..."

2013-11-18T14:24:12Z

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..."

New page

==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/
* Instructions for using TBA are here: http://www.bx.psu.edu/miller_lab/dist/tba_howto.pdf
* A phylogenetic tree is a required input.
* Three are 3 steps required to run TBA:
## Generate a series of pair-wise alignments to “seed” the multiple alignment process.
Example: all_bz - "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" blastz.specs >&all_bz.log
## Generate the multiple alignment
Example: tba "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" *.*.maf tba.maf >&tba.log
## "project" the alignment onto a reference sequence. This will not make it a reference-based alignment; it just allows for visualization.
## Example: maf_project tba.maf chicken > tba_project_chicken.maf

==Loading .maf files into GenomeView==
*Once you have a .maf multiple alignment, projected onto a reference genome, you can load this into GenomeView.
*First, verify that all contig ID’s used in the .maf file match the contig ID’s used in your genome sequence and annotation files. Load the genome sequence, annotation, and .maf file with matching contig ID’s into Genomeview.
*In order to view comparative annotations, you need to follow these steps:
** Enable comparative annotations:
Under “File”, select “Configuation”.
Select the tab for “Comparative track”.
Make sure the box for “Enable comparative annotations” is checked.
## Load in one annotation file for each genome in your multiple alignment (checking to make sure all contig ID’s match those used in the .maf file).
## You should now see annotations for each genome in the multiple alignment.

@@ Line 15: / Line 15: @@
 In order to view comparative annotations, you need to follow these steps:
-* 	Enable comparative annotations: <pre>Under “File”, select “Configuation”.<br/>Select the tab for “Comparative track”.<br/>Make sure the box for “Enable comparative annotations” is checked.</pre>
+* 	Enable comparative annotations:
-# Load in one annotation file for each genome in your multiple alignment (checking to make sure all contig ID’s match those used in the .maf file).
+**Under “File”, select “Configuation”.
-# You should now see annotations for each genome in the multiple alignment.
+**Select the tab for “Comparative track”.

@@ Line 10: / Line 10: @@
 ==Loading .maf files into GenomeView==
-*Once you have a .maf multiple alignment, projected onto a reference genome, you can load this into GenomeView.
+Once you have a .maf multiple alignment, projected onto a reference genome, you can load this into GenomeView.
-*First, verify that all contig ID’s used in the .maf file match the contig ID’s used in your genome sequence and annotation files.  Load the genome sequence, annotation, and .maf file with matching contig ID’s into Genomeview.
-*In order to view comparative annotations, you need to follow these steps:
+First, verify that all contig ID’s used in the .maf file match the contig ID’s used in your genome sequence and annotation files.  Load the genome sequence, annotation, and .maf file with matching contig ID’s into Genomeview.
-** 	Enable comparative annotations:
- Under “File”, select “Configuation”.
+In order to view comparative annotations, you need to follow these steps:
- Select the tab for “Comparative track”.
+* 	Enable comparative annotations: <pre>Under “File”, select “Configuation”.
- Make sure the box for “Enable comparative annotations” is checked.
+Select the tab for “Comparative track”.
-## Load in one annotation file for each genome in your multiple alignment (checking to make sure all contig ID’s match those used in the .maf file).
+Make sure the box for “Enable comparative annotations” is checked.
-## You should now see annotations for each genome in the multiple alignment.
+</pre>

@@ Line 5: / Line 5: @@
 * A phylogenetic tree is a required input.
 * Three are 3 steps required to run TBA:
-# Generate a series of pair-wise alignments to “seed” the multiple alignment process.
+# Generate a series of pair-wise alignments to “seed” the multiple alignment process.  <pre>Example:  all_bz - "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" blastz.specs >&all_bz.log</pre>
- Example:  all_bz - "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" blastz.specs >&all_bz.log
+# Generate the multiple alignment <pre>Example:  tba "(((((((human chimp) gorilla) baboon) (rat mouse)) (cow pig)) chicken) fugu)" *.*.maf tba.maf >&tba.log</pre>
 # "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>