--quantMode GeneCounts for gene families

alexdobin / STAR

RNA-seq aligner

MIT License

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--quantMode GeneCounts for gene families #746

Open CuypersBart opened 5 years ago

CuypersBart commented 5 years ago

Hi,

I used --quantMode GeneCounts to generate a count table for my samples, after which I processed them with DESEQ2.

I noticed that a whole gene family is differentially expressed. (I think) This typically happens when reads are randomly divided over family members when they are being mapped. Is there any way to avoid these multimappers to be counted? I would rather only look at uniquely mapping reads to get gene specific information.

Best Regards,

Bart

alexdobin commented 5 years ago

Hi Bart,

--quantMode GeneCounts only counts unique mappers, so the must be enough sequence difference between these genes to allow for unique mapping.

Cheers Alex