STAR aligned reads minimum maping quality
I aligned RNAseq data with GRCH 37 and wonder what cut off of read quality is generally used when we perform downstream analysis. I know in HISAT2 generally read quality >20 is considered. I could not find any general rule of quality cutoff in STAR. Any suggestion?
• 4,479 views
•
link
updated
by
caggtaagtat
•
written
by
rob.costa1234
•
written
by
rob.costa1234
2 answers
Take a look at this blog post by Dr. Simon Andrews and decide for yourself.
Like mentioned in the blog post of genomax, I always go with the cutoff of 255, resulting in only uniquely mapped reads.
• 0 views
•
link
written
by
caggtaagtat
Log in to answer this question.
More posts like this
-
Pre-Alignment process
written by AIMAR •
-
Reference Genome with decoy for RNAseq data processing
written by cwwong13 •
-
Need Guidance regarding WGCNA
written by ML •
-
Does StringTie need strand information if HISAT2 was run with strand-specific information
written by piyushjo
-
"high" quality RNA but poor RNAseq results
written by CrazyB
-
for low coverage RNAseq how many reads assigned is the bare minimum for differential gene expressio…
written by senowinski •
-
singleton reads RNAseq downstream analysis
written by prasundutta87
-
Adapter Trimming Length Cutoff And Quality Trimming Quality Cutoff
written by epigene
-
Cutoff For Broad Peaks For Macs2 Peakcaller
written by Dataminer
-
What Is A Typical Quality Cutoff When Trimming Rnaseq Data?
written by camelbbs
I guess you are talking about differential expression analysis, but it doesn't hurt to be specific...