I have often read (and anecdotally confirmed) that adapter removal, quality trimming and such are not necessary for simple estimation of transcript relative abundance in a pseudoalignment framework. My tool of choice is Kallisto, and I am doing bulk RNAseq on a NextSeq, for context.
When low quality matches are going to be discarded, is there a point in actually quality filtering reads? Certainly it's going to reduce the number of mismatches. Assuming one is willing to accept background noise in exchange for more depth/coverage, the tradeoff could be worth it (eg, in the case of a quality bias towards a few samples).
A middle ground could be disabling quality filtering but performing trimming instead, but I imagine that might end up with a lot of very short reads that you might have to reject to avoid them matching all over the place...
Anyhow, I would appreciate advises/explanations or general thoughts