Hi @all,
I have a problem in understanding some alignments produced by BWA mem (Version: 0.7.8-r455):
1) Besides the obvious (all alignments are crap)... is MapQ influenced by clipping at all? Why not? What about other aligners?
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!
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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