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?
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caggtaagtat
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rob.costa1234
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rob.costa1234
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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.
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