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STAR aligner options for unstranded RNA-seq

I plan to do STAR-htseq using an unstranded RNA-seq dataset. I can only find in the manual that the option --outSAMstrandField intronMotif is needed for cufflinks only. It's not clear to me if I need to specify that option or any other option specific for unstranded data in order to use other quantification tools such as htseq.

rna-seq alignment next-gen star aligner
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updated by Devon Ryan Devon Ryan • written by fana • fana

1 answer

You don't need to specify anything for it to be compatible with htseq-count.

Note that featureCounts is faster than htseq-count and that STAR can also do unstranded quantification (it's also faster than htseq-count).

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written by Devon Ryan Devon Ryan

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