STAR parameters for mapping single-cell data Smartseq2

alexdobin / STAR

RNA-seq aligner

MIT License

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STAR parameters for mapping single-cell data Smartseq2 #1456

Open Anara2018 opened 2 years ago

Anara2018 commented 2 years ago

Dear Alex, I am currently running the STAR pipeline (with featurecounts afterwards) for single-cell mapping with Smartseq2 data, and I was wondering it these parameters seem reasonable:

alexdobin commented 2 years ago

Hi @Anara2018

these parameters look good. You do not really need --sjdbOverhang, sine you are not supplying GTF at the mapping step. If you used GTF at the genome generation step, you need to specify this parameter at that step.

Cheers Alex