- Not directly, see a discussion here.
- Maybe decrease -B, though I worry that this will just decrease the reliability of alignments. It'd be better to just blast things.
- Nope, as Brian suggested, I'd blast the soft-clipped portions of a few reads.
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1) BBMap's map scores are not directly affected by the bases in the clipped portion, though they are affected by the length of the aligned portion, so 100= would score slightly higher than 50=50S. Also, shorter alignments are more likely to be coincidentally ambiguous so they will tend to have a slightly lower score. That said, clipping is disabled by default as BBMap is a global aligner. For BWA, I don't know how the score is calculated.
3) I've seen alignments like that when mapping to the wrong reference (e.g. contaminant reads). You might want to gather some of those mostly-clipped reads and blast them to nt; that may give you insight into how to filter them. Also, if a read starts out normal then becomes junk (for example, short-insert read that hits adapter sequence and then random letters, or a PacBio read where the enzyme breaks down partway through) you get those local alignments with most of the read clipped.
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Mapping quality and clipping in BWA
Hi @all,
I have a problem in understanding some alignments produced by BWA mem (Version: 0.7.8-r455):
Code:IQ4WJ2H02II3G5 0 chromosome_1 256920 60 512S33M * 0 0 IQ4WJ2H02GYKYP 0 chromosome_1 380024 12 312S33M142S * 0 0 IQ4WJ2H01BLH7R 16 chromosome_1 794344 7 79M178S * 0 0
2) Next question would be if it is possible to prevent things like this from happening? I tried to adjust the "-L" parameter but it seems to have almost no effect - I tried standard (5), 50, 100, 10000 and these alignments occur in all 4 runs.
3) Has anyone of you ever seen something like this before? How do you handle/filter these reads then? The only thing that occurs to me is selecting by S/H with values greater than 50(?),100(?),10% read length(?)
Any suggestion helps!
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