IDT Targeted Panels

[pintoa1-mskcc]

Hi all,

My group is developing a pipeline and we frequently encounter standard ribo-depleted RNA sequencing panels, as well as IDT targeted panels. To that end, how does salmon handle on and off target quantifications? Would it be best to assume that any off target transcripts are "low quality" calls and we should remove them from analysis?

Is there any incoming updates or features you all may be thinking of to account for targeted captures of RNA?