Question: mapping quality for sanger reads
gravatar for shinken123
2.0 years ago by
shinken12310 wrote:


Anyone knows if BWA-mem automatically detect if the reads that I am aligning have their quality is fastq-sanger?. If not, this affect the mapping quality score?


alignment • 618 views
ADD COMMENTlink modified 2.0 years ago by Biostar ♦♦ 20 • written 2.0 years ago by shinken12310
gravatar for Ashutosh Pandey
2.0 years ago by
Ashutosh Pandey11k wrote:

BWA aln provides -I option that can be used to align fastq reads with Phred+64 quality scores. The reads in output bam file have base quality in Sanger or Phred+33 format.  BWA-mem doesn't have that option (at least not stated in the manual). If you search on this forum there are multiple posts that explain in detail about how to test if reads belong to Phred+33 or Phred+64. Also, you can easily convert them from one to other.  Base quality scores are not used in the calculation of mapping quality scores but BWA mem may throw an out of range error if it can't take Phred+64 fastq files. 

ADD COMMENTlink written 2.0 years ago by Ashutosh Pandey11k

Thank you very much. So if my reads are from a sanger sequencing (Phred+33) and BWA-mem assumes that the sequences are in Phred+33, is going to work fine with my data.

Thanks again


ADD REPLYlink written 2.0 years ago by shinken12310
Well if your reads are phred+33 then you don't need to do anything. Just use BWA mem.
ADD REPLYlink written 2.0 years ago by Ashutosh Pandey11k
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