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areyesq89 / DEXSeq

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No counts where there should be counts #14

Closed mibsmibs closed 2 years ago

mibsmibs commented 2 years ago

I have a data set that has counts over our gene of interest using DESeq but no counts at all over the same region using DEXSeq. Do you know how this could be? Is there an internal filter in the DEXSeq call?

areyesq89 commented 2 years ago

Very likely. If paired-end, DEXSeq htcount script required both fragments to be mapped correctly and to be uniquely mapping. Either of these steps might be discarding read from being counted.