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Uniquely Mapping Reads are overestimated #80

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Rohit-Satyam opened this issue May 7, 2023 · 1 comment
Open

Uniquely Mapping Reads are overestimated #80

Rohit-Satyam opened this issue May 7, 2023 · 1 comment
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@Rohit-Satyam
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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
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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))

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@agraubert @Rohit-Satyam