I have been using Salmon to align QuantSeq reads to the human transcriptome and have been coming up with ~40-60% mapping rates for all of my samples. I have run the reads through quality control for min Phred scores, minimum lengths, and decontamination with no luck at improving the mapping rates. I am very new to using QuantSeq data and am curious if this is typical for human transcriptome alignments, or if these rates are low enough to be worried. Long term, I am hoping to perform differential gene expression on these samples, and want to make sure I am not missing anything with the alignment step.
Thanks for your help!