strand-specific RNA-seq analysis

Question

[17318598206]

my RNA-seq data :Total RNA (1μg) from each cell type was used to generate next generation RNA-seq libraries using Illumina TruSeq stranded library preparation kit per manufacturer’s protocol by RNA ligation method, so, when i use HTseq-count to gain read counts, for -s yes/no/reverse, which should i choose,and why

[Zhenyu Zhang]

When in doubt, try all of them. Btw, since STAR aligner can generate STAR Count with all 3 options in one run, I don't see the benefit of using HTSeq.

[17318598206]

so, how to use STAR to generate STAR Count with all 3 options in one run

[Zhenyu Zhang]

It's by default and done together with alignment. Check this post RNA-seq: Explain STAR quantMode geneCounts values