Question: STAR aligner options for unstranded RNA-seq
0
gravatar for fana
8 months ago by
fana0
London
fana0 wrote:

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.

ADD COMMENTlink modified 8 months ago by Devon Ryan90k • written 8 months ago by fana0
1
gravatar for Devon Ryan
8 months ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

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).

ADD COMMENTlink modified 8 months ago • written 8 months ago by Devon Ryan90k
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