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getzlab / rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization
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mapping quality argument #69

Closed NomiCentarix closed 2 years ago

NomiCentarix commented 2 years ago

Hi,

All the reads in my bam file have a mapping quality of 255. I ran the rnaseqc with the mapping quality argument set to 0, but still the "High Quality Reads" metric resulted is 0. Why?

Thanks, Nomi

agraubert commented 2 years ago

High Quality Reads also filters out reads with more than 6 mismatches. You can try setting the mismatch threshold to something higher to see if that changes your output