I'm comparing three different QC tools (trimgalore, trimmomatic, & bbduk) and then seeing how STAR alignments are affected by all of them, comparing against a noQC run. Specifically, I am comparing the "AS" and "nM" fields in the BAM file. I figured that the alignment scores should increase, but the QC file without any QC gets the best alignment scores, albeit with higher mismatch rates.
I am concerned that the alignments after QC may be worse because of this, specifically the means of the alignment scores can be seen:
trimgalore - noQC = -5.57 trimmomatic - noQC = -2.99 bbduk - noQC = -1.15
Why are the QC tools causing worse alignment scores in STAR?