DEGseq and uniquely mapped reads

[PFS]

I have topHat-mapped reads that I converted to bed format so that I can pass it to DEGseq.

How can I make sure the reads are uniquely mapped, as requested by DEGseq? Should I re-run Bowtie or DEGseq takes care of that?

Thanks!

[Xi Wang]

Sorry for the late reply. You may use the converted bed files to feed DEGseq. DEGseq suggests to discard the reads that map to multiple loci, but discarding all the multi-reads may not be the best choice.