STAR aligned reads minimum maping quality

Question

[rob.costa1234]

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?

[WouterDeCoster]

when we perform downstream analysis.

I guess you are talking about differential expression analysis, but it doesn't hurt to be specific...

Answer 1

[GenoMax]

Take a look at this blog post by Dr. Simon Andrews and decide for yourself.

Answer 2

[caggtaagtat]

Like mentioned in the blog post of genomax, I always go with the cutoff of 255, resulting in only uniquely mapped reads.