Is it possible to set minimum coverage?

[690645258]

Hi folks,

I'm trying to use salmon to quantify viral and bacterial pathogens in transcriptomic samples. However when doing this I'm getting some counts for various viruses where reads are mapping to a single poly(a) or poly(t) region only, the remainder of the transcript has no coverage but is still counted as a read for that transcript.

Is there any way to set a minimum amount of coverage of each transcript for it to be accepted as a viable transcript? E.g I want a transcript to have at least 50% coverage before it is counted?

Cheers!

[Rohit-Satyam]

I ended up having a similar issue where my parasite RNASeq data had contamination from Green Monkey which resulted in lot of multimapping reads and when I run Salmon on such bam files followed by differential analysis I get 300 new DEGs upregulated and 200 new genes that are down regulated. I have a reason to believe that such cases need to be checked and reads should be removed prior to alignment so that salmon doesn't get confused about it.