I made a RNAseq library using a stranded-RNAseq-library prep kit. The kit only amplifies the transcript strand. I then aligned the paired-end fastq's using HISAT2 using the option for "stranded" and FR (forward read). Typically I use featureCounts to count the genes but I now need strand orientation info in my featureCounts table.
My question is how do I get strand info?