How to get unaligned reads with bowtie for each entry files

[Sebastien]

Hi, I come here again with a question. I'm wondering if their is a way to get the unaligned reads from bowtie with one file per entry files?

Thank you Sebastien

[Eduardo Andres Leon]

Hi, You can use samtools (provided along with miARma) to do it, for example:

miARma/bin/Linux/samtools/samtools view -f 4 SRR873382_nat_bw1.bam

(I'll try to answer your other issue this week)

[Sebastien]

Thank you for your answer i'll try that. No problem. Thank you very much