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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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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