Question: STAR Alignment Score reduced after trimming
0
gravatar for dec986
9 months ago by
dec986130
United States
dec986130 wrote:

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?

rna-seq star • 512 views
ADD COMMENTlink modified 9 months ago by Devon Ryan86k • written 9 months ago by dec986130
4
gravatar for Devon Ryan
9 months ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

There's little point in trimming reads with STAR (or other tools that do local alignment), at most trim adapters and very low quality bases (phred scores up to ~3 or so). Presuming you did quality trimming, it's likely that the score you used was much too high, which decreased the number of bases that STAR would have otherwise aligned and therefore decreased the alignment scores. Even adapter trimming isn't perfect, since inevitably you'll end up trimming off a bit of sequence. For both our command line and Galaxy RNAseq workflows, we skip trimming entirely and use STAR with the raw reads. That tends to produce quite nice results.

ADD COMMENTlink modified 9 months ago • written 9 months ago by Devon Ryan86k

thank you! who is "our"?

ADD REPLYlink written 9 months ago by dec986130
1

who is "our"?

@Devon is currently a bioinformatician/data manager at the Max Planck Institute for Immunobiology and Epigenetics in Freiburg, Germany.

ADD REPLYlink written 9 months ago by genomax58k

great, thanks, I have to let my colleagues know. We're comparing several different RNA-Seq pipelines.

ADD REPLYlink written 9 months ago by dec986130

Evidently a great manager too

ADD REPLYlink written 9 months ago by Kevin Blighe32k
1

Thankfully I manage the data and not the people :)

ADD REPLYlink written 9 months ago by Devon Ryan86k

Is there any official documentation for this? I can't find anything in google searches or in the STAR manual

ADD REPLYlink written 3 months ago by dec986130
1

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.

ADD REPLYlink written 3 months ago by Devon Ryan86k
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