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STAR --quantMode GeneCounts function

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
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updated by Ram Ram • written by linjc.xmu • linjc.xmu

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

• 1 views • link
written by grant.hovhannisyan grant.hovhannisyan

2 answers

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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written by Pin.Bioinf Pin.Bioinf

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

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written by h.mon h.mon

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