Preparing value data - Revision history

69.173.108.66 at 18:41, 14 May 2014

2014-05-14T18:41:41Z

Thomas Admin: /* SAMTools pileup (includes diversity information, i.e. SNP track) */

2013-11-15T18:47:23Z

SAMTools pileup (includes diversity information, i.e. SNP track)

69.173.108.246: /* Creating TDF files */

2013-11-15T18:34:06Z

Creating TDF files

69.173.108.246: /* SAMTools pileup (includes diversity information, i.e. SNP track) */

2013-11-15T18:33:52Z

SAMTools pileup (includes diversity information, i.e. SNP track)

69.173.108.246 at 18:33, 15 November 2013

2013-11-15T18:33:22Z

69.173.108.246 at 18:31, 15 November 2013

2013-11-15T18:31:38Z

Thomas: Created page with "TDF is a binary file format that contains preprocessed summary information for display in a genome browser. This format is an alternative to wig and the bigwig formats and is..."

2013-10-18T15:02:47Z

Created page with "TDF is a binary file format that contains preprocessed summary information for display in a genome browser. This format is an alternative to wig and the bigwig formats and is..."

New page

TDF is a binary file format that contains preprocessed summary information for display in a genome browser.

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.

You can create TDF files directly from BAM files or from wig files.

== Creating TDF files ==
* [[bam2tdf]]: convert read alignment to coverage plot
* [[wig2tdf]]: convert wig formatted data to tdf formatted data

@@ Line 15: / Line 15: @@
 The first step to be able to browse a pileup is to generate one from your BAM file.
-  samtools pileup -f reference.fasta  sorted.bam >sorted.pileup
+  samtools mpileup -f reference.fasta  sorted.bam >sorted.pileup
 As you run this command, you'll see that the generated file can be huge, even for small BAM files.

@@ Line 26: / Line 26: @@
-<h2>Tab delimited pileup (extension should contain '.swig')</h2>
+==Tab delimited pileup (extension should contain '.swig')==
 The file should be organized in four columns.
 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.
@@ Line 52: / Line 52: @@
 It is recommended that you convert this format to TDF with [[wig2tdf]].
-<a href="http://sourceforge.net/projects/samtools/files/samtools/">Download samtools</a>
+[http://sourceforge.net/projects/samtools/files/samtools/|Download samtools]
-<a href="https://sourceforge.net/projects/samtools/files/tabix/">Download tabix</a>
+[https://sourceforge.net/projects/samtools/files/tabix/|Download tabix]

@@ Line 15: / Line 15: @@
 <em>Note: file name extension should contain .pileup</em>
 The first step to be able to browse a pileup is to generate one from your BAM file.
-<code>
-samtools pileup -f reference.fasta  sorted.bam >sorted.pileup
+ samtools pileup -f reference.fasta  sorted.bam >sorted.pileup
-</code>
 As you run this command, you'll see that the generated file can be huge, even for small BAM files.
 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.
-<code>
-sort -k1,1 -k2,2n sorted.pileup | bgzip -c > compressed.pileup.bgz
+ sort -k1,1 -k2,2n sorted.pileup | bgzip -c > compressed.pileup.bgz
-tabix -s 1 -b 2 -e 2 compressed.pileup.bgz
+ tabix -s 1 -b 2 -e 2 compressed.pileup.bgz
-</code>
 <h2>Tab delimited pileup (extension should contain '.swig')</h2>
@@ Line 38: / Line 38: @@
 Example:
-<code>
+ chr1	11	46	43
-chr1	11	46	43
+ chr1	12	47	50
-chr1	12	47	50
+ chr1	13	48	61
-chr1	13	48	61
+ chr1	14	53	79
 chr1	14	53	79
 <em>Note that the white-space between the columns are tabs, one tab between each column</em>.
 Once you have such a file, you can again index it for faster access and shorter download times.
-<code>
-sort -T . -k1,1 -k2,2n filename | bgzip -c > filename.bgz
+ sort -T . -k1,1 -k2,2n filename | bgzip -c > filename.bgz
-tabix -s 1 -b 2 -e 2 filename.bgz
+ tabix -s 1 -b 2 -e 2 filename.bgz
-</code>
 It is recommended that you convert this format to TDF with [[wig2tdf]].

@@ Line 12: / Line 12: @@
+== SAMTools pileup (includes diversity information, i.e. SNP track) ==
 <em>Note: file name extension should contain .pileup</em>
 The first step to be able to browse a pileup is to generate one from your BAM file.
@@ Line 57: / Line 52: @@
 </code>
-<h2>Resources</h2>
+It is recommended that you convert this format to TDF with [[wig2tdf]].
 <a href="http://sourceforge.net/projects/samtools/files/samtools/">Download samtools</a>
 <a href="https://sourceforge.net/projects/samtools/files/tabix/">Download tabix</a>

@@ Line 7: / Line 7: @@
 You can create TDF files directly from BAM files or from wig files.
-== Creating TDF files ==
+== Creating TDF files (recommended)==
 * [[bam2tdf]]: convert read alignment to coverage plot
 * [[wig2tdf]]: convert wig formatted data to tdf formatted data
 == SAMTools pileup (includes diversity information, i.e. SNP track) ==

@@ Line 1: / Line 1: @@
-TDF is a binary file format that contains preprocessed summary information for display in a genome browser.
+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.
 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.
@@ Line 8: / Line 10: @@
 * [[bam2tdf]]: convert read alignment to coverage plot
 * [[wig2tdf]]: convert wig formatted data to tdf formatted data