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getzlab / rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization
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Uniquely Mapping Reads are overestimated #80

Open Rohit-Satyam opened 1 year ago

Rohit-Satyam commented 1 year ago

Hi Developers

I observe that the Uniquely mapping read percentage provided by rnaseqc is huge as compared to the "Uniquely mapped reads %" reported by STAR _Log.final files. Is your Unique Rate of Mapped number calculated differently? For Example

An exemplary output of STAR and rnaseqc of a sample is attached below:

batch2.zip

agraubert commented 1 year ago

RNA-SeQC computes "Unique Rate of Mapped" as the ratio between reads with the following flags: ( Mapped & ~ (Secondary | QCFail | Supplementary | Duplicate)) over ( Mapped & ~ (Secondary | QCFail | `Supplementary))