Tweet
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!
-
-
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
-
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
-
Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...09-23-2024, 06:35 AM -
During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.
Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...09-09-2024, 10:59 AM
Comment