STAR --quantMode GeneCounts function
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3.7 years ago
linjc.xmu ▴ 30

Dear all,

Does STAR 2.6 --quantMode GeneCounts only quant unique mapping reads? How to specialize it only quant the unique mapped reads?

Thanks a lot.

RNA-Seq • 4.6k views
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yes, it works exactly like HTSeq count with union option.

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3.7 years ago
Pin.Bioinf ▴ 300

Yes, and you will have to choose a column among the results, please refer to RNA-seq: Explain STAR quantMode geneCounts values

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3.7 years ago
h.mon 34k

Usa, STAR with --quantMode GeneCounts includes only uniquely mapped reads in the quantification.

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