view tools/mytools/bowtie2bed.xml @ 1:cdcb0ce84a1b

author xuebing
date Fri, 09 Mar 2012 19:45:15 -0500
parents 9071e359b9a3
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<tool id="bowtie2bed" name="bowtie-to-bed">
  <description> converter and read extender</description>
  <command interpreter="perl"> $input $out_file1 $extendLength </command>
    <param name="input" format="txt" type="data" label="Bowtie map result file"/>
    <param name="extendLength" size="10" type="integer" value="200" label="Extend 3 primer (bp)"/>
    <data format="bed" name="out_file1" />
      <param name="input" value="" ftype="TXT"/>
      <param name="extendLength" value="200"/>
      <output name="out_file1" file="testmap.bed"/>

**What it does**

This tool converts bowtie output map format file to bed format, with the option to extend the 3 primer end.

- Sequence and quality information is lost after conversion
- The output contains a track name at the first row



Converting the following bowtie mapped reads::

  SRR073078.2 HWUSI-EAS465_8_1_1_524 length=36	-	chr2	112499209	AGTGTGACTGCATCTCTTCCTTCGTGGGGCTNCAGT	...
  SRR073078.3 HWUSI-EAS465_8_1_1_1054 length=36	+	chr17	75877120	CCACNCCTCCTTTCAAAACACACTGCCAGGTGCGTC	...

will result in::

  track name=/home/xuebing/Research/galaxy/galaxy-dist/database/files/000/dataset_5.dat itemRgb=On
  chr2	112499109	112499245	SRR073078.2-HWUSI-EAS465_8_1_1_524-length=36	1	-	112499209	112499245	0,255,0	
  chr17	75877120	75877256	SRR073078.3-HWUSI-EAS465_8_1_1_1054-length=36	1	+	75877120	75877156	255,0,0