After I use the "-q 20" option in bwa aln I start getting errors down the road eg when i run ValidateSamFile in picard I get lots of "Mate negative strand flag does not match read negative strand flag of mate" and then "Sequence and quality are inconsistent" errors as well. I have run all the same commands without the -q option without these problems. I am very new to all this and not sure where I'm going wrong!
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A little late, but I am also running -q option and curious if you identified the problem. -
No I ended up just running it without trimming as I decided it wasn't really necessaryComment
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This is a bug in BWA. If you use -q it puts the trimmed nucleotide read in the output SAM file but the quality sequence is not trimmed at all and thus there is a difference in the length of the read and the length of the quality string. Either use some third party tool like trimgalore to trim your fastq reads before aligning and don't use BWA -q option at all OR use some script that takes SAM file and trims off the base quality string accordingly.
PS:This post may help- http://www.biostars.org/post/show/13...or-space-data/Comment
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The immune system’s power comes from its genetic diversity, allowing myriad threats to be neutralized through first recognizing foreign antigens. That diversity is also what makes the immune system so difficult to study. Recent advances in sequencing technology and computational biology, however, are giving researchers new tools to understand immune responses and immune-related diseases in greater detail.
This convergence of genetics, immunology, and computation...09-01-2026, 05:41 AM
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