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Old 09-27-2011, 10:47 PM   #1
Location: US

Join Date: Mar 2010
Posts: 25
Unhappy Bowtie .sam and .map output difference?

Hello everyone,

I'm trying to map RNAseq reads to the known genome and my search resulted in 2 commands giving different output. Both are supposedly alignments to the reference file but one is a .sam file while other is a .map file. Are these both same ones and the sam file is just different extension? Following are the commands which I used,

bowtie --sam reference sample.fa aligned_reads.sam

and the other one is,

bowtie reference sample.fastq >

Which of the these files can I use as input for DEGseq? I am a newbie to all this and I would really appreciate any help.

Thanks in advance,

Kaustubh Gokhale.
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Old 09-27-2011, 11:25 PM   #2
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Location: Canada

Join Date: Nov 2010
Posts: 124

Bowtie can output aligned reads in either its default .map, or .sam format. They contain basically the same data, but in different formats. I think in general, most downstream programs would use .sam. I've never used DEGseq. Also, I've only done ChIP-seq not RNA-seq, but I think it's better to use Tophat for RNA-seq, instead of using Bowtie directly.
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Old 09-28-2011, 11:17 AM   #3
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Join Date: Mar 2010
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Thanks biznatch!
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bowtie, map, output, sam

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