Working with bowtie legacy output

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7.8 years ago

YanO ▴ 140

Hi all,

I currently am working with some old data, from 2010. It is in what I think is the old legacy bow tie output. The file extension is sample1.bowtie.align.txt.gz. Does anyone know how to convert this format into a different format? I'll take literally any other format: sam/bam/fastq/bigwig.... I can't seem to find anything that accepts the current format. The only thing I have found so far is a bowtie2sam.pl script, but I got it from https://github.com/lh3/samtools-legacy/blob/master/misc/bowtie2sam.pl but this folder has the description "For testing only. DON'T USE!" so I'm a bit worried about that.

The first few lines are as follows:

WICMT-SOLEXA2_3_203EJAAXX_1_1_118_272   +   chr9    3035086 TTTTCAGTTTTCTTGCCATATTCCAT  IIIIIIIIIIIIIIIIIIIIIIIIII  67  
WICMT-SOLEXA2_3_203EJAAXX_1_1_118_272   +   chr5    3001564 TTTTCAGTTTTCTTGCCATATTCCAT  IIIIIIIIIIIIIIIIIIIIIIIIII  67  
WICMT-SOLEXA2_3_203EJAAXX_1_1_122_533   +   chr5    3002103 TCATTTTTCAAGTCGTCAAGTGGATG  IIIIIIIIIIIIIIIIIIIIIIIIII  11

bowtie alignment • 1.1k views

ADD COMMENT • link updated 7.8 years ago by Devon Ryan 104k • written 7.8 years ago by YanO ▴ 140

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Entering edit mode

Here's a thread on SEQanswers (scroll down to the post from Nick) with a modified version of that perl script that should work a bit better.