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Old 11-19-2009, 05:54 PM   #1
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Location: Xishuangbanna

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Default Bowtie output

Hi there~

I have some questions about the output setting of Bowtie.

1. Can I get separate output files in relation to input files? I tried to put comma separated filenames but that does not work.

2. I tried --al<filename>, but it only writes the reads, not the alignment. Is there something to do to get alignment?

3. for the option --refout, why it will output so many file? one map one alignment?

Thanks very much
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Old 11-20-2009, 03:31 AM   #2
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

1. An easy way is to wrap your bowtie command in a shell for loop:

for i in *fastq
bowtie --best /some/genome/index $i > $i.bowtie.txt

2. That option allows you to separate the reads which aligned from those which don't and corresponds to un for unaligned reads and max for multiply aligning reads. It's not really designed to report alignments.

3. Sorry, no idea - never used that one.
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Old 11-20-2009, 05:07 AM   #3
Ben Langmead
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Location: Baltimore, MD

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Posts: 200

Originally Posted by pythonlovesbowtie View Post
3. for the option --refout, why it will output so many file? one map one alignment?
There's 1 output file per input sequence. If you have an input file with 1000 sequences in it, that's 1000 distinct output files. If you have a ton of input files, this clearly may not be what you want.

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