Hello, We have used ovation RNA-seq system and prepared some libraries. We have sequenced single-ends. We want to use hisat2 and htseq counts to get counts per gene in our organism. I wondered if someone has worked with this before, what parameter should be specificied in rna-strandness on HISAT2 parameters.
Also,I understand that parameter determines whether a read correspond to a transcript, or to the reverse complemented counterpart of a transcript. But afterwards, in htseq-count, the stranded parameter depends also on this? I mean, if we use --rna-strandness F in hisat2, then we have to use --stranded yes or --stranded reverse in htseq-count?
Thanks for your help