I'm working with RNA-seq data. For the analysis I will be using HISAT2 to align sequencing reads to the human genome GRCh38. Samples are subjected to strand-specific RNA sequencing using poly-A selection protocol and sequenced on the Illumina HiSeq 2000 system. They are paired-end reads.
I would like to know how the Hisat2 command need to be given for strand-specific option.
--rna-strandness should be RF or FR