[Samtools-help] questions about pileup

[Chunjiang He <cam...@gm...>]

Hi,

I just want to ask if samtools pileup can give the reads counts in refseq
gene region. Should I first get all counts in the whole genome and then
calculate the counts in gene region by myself? Can samtools do the same
thing as Htseq-count?

Thanks,

Chunjiang