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.
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.
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