Salmon PacBio

[Anne Ndungu]

Hi,

I'm trying to use Salmon to quantify pacBio reads. While doing a sanity check for transcripts that I know should not be present, I notice them to have high TPMs. I think due to some 5' end fragmented reads that are missing the first few exons while the rest match to my transcript that should not be present. Is there a way to account for this in Salmon to improve the counts using the quasi-mapping?

Best wishes,

Anne