ht-seq count

[FLYINGDOLPHIN]

Hi,

I am using htseq-count to count the reads before using DeSeq.

I am not sure whether I need to use the option -m nonempty or union.

Does this affect the result of Deseq analysis?

Thanks.

Q

[sdriscoll]

I think it follows necessarily that if your counts are different the the differential expression could be different. I don't think there is necessarily a correct answer though. If in doubt, use the default settings.