STAR --quantMode GeneCounts function

Question

[linjc.xmu]

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.

[grant.hovhannisyan]

yes, it works exactly like HTSeq count with union option.

Answer 1

[Pin.Bioinf]

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

Answer 2

[h.mon]

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