Thank you, Devon! Very helpful.
• 0 views
•
link
written
by
grant.hovhannisyan
Mapping Quality of reads with mismatches in STAR
Dear All,
STAR mapper by default assigns MAPQ 255 for uniquely mapped reads. However, read can map uniquely, but have mismatches (due to SNVs and indels). I am wondering how mismatches influence the mapping quality in this case. In other words, does the uniquely mapped read with mismatches have MAPQ 255?
Thanks,
• 3,162 views
•
link
updated
by
Devon Ryan
•
written
by
grant.hovhannisyan
•
written
by
grant.hovhannisyan
1 answer
Any read that has a single "best" alignment will have a MAPQ of 255. Containing mismatches, be they SNVs or InDels, does not change that.
• 0 views
•
link
written
by
Devon Ryan
Log in to answer this question.
More posts like this
-
Asking for unmapped genes in RNA sequencing via Galaxy
written by Atefeh •
-
Which threshold to be put in the MAPQ when doing mpileup of BCF tools on a STAR-generated BAM file ?
written by mohsamir2016 •
-
Better understanding of STAR statistical summary
written by mohsamir2016 •
-
Differences in unique mapping between STAR and BLAST?
written by steel1990 •
-
Counting uniquely mapped reads - ambiguous results
written by mickey_95 •
-
STAR mapping statistics don't add up with samtools count
written by Zee_S
-
Bowtie2 - How can MAPQ be used to obtain uniquely mapped reads?
written by ej
-
RSEM for xenograft samples: augmented genomes and multi-mapped reads
written by NaskoMak •
-
Should I include ambiguously mapped reads in the realignment around InDels?
written by stu111538
-
HISAT2 (v2.0.0-beta) MAPQ query for allele specific expression analysis
written by prasundutta87
