I've just received TRC2 shRNA library data and have been tasked to quantify the number of reads that map back to each insert. Would it be appropriate to use Salmon for this task? After trimming all the reads down to the same spot where the insert is supposed to be (found by grepping the flanking sequence) I created a Salmon TRC2 index and ran it using the same settings I usually use for RNA-Seq. This does indeed work to an extent as I do get counts, however I'd like to get a second opinion on how to make sure I am actually capturing as many true counts as possible. For example, I'm sure my trimming caused me to lose quite a few reads since some inserts were a base or two off of the expected position. However, if I don't trim super conservatively it seems that Salmon has trouble mapping them.
