Hello,
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?
thank you! who is "our"?
@Devon is currently a bioinformatician/data manager at the Max Planck Institute for Immunobiology and Epigenetics in Freiburg, Germany.
great, thanks, I have to let my colleagues know. We're comparing several different RNA-Seq pipelines.
Evidently a great manager too
Thankfully I manage the data and not the people :)
Is there any official documentation for this? I can't find anything in google searches or in the STAR manual
That's not going to be documented since it's not a direct result of a tool, but rather an interaction between how alignments work generally and trimming generally changes thing.