Bowtie .sam and .map output difference?

[kasutubh]

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 > sample.map

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.

[biznatch]

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.

[kasutubh]

Thanks biznatch!