I have RNA-seq data made from Illumina TruSeq Stranded mRNA Sample Preparation Kit. Some of my samples are paired end, however one set is single end. I have already processed the paired end ones, and understand to use 'reverse-strand' or -s 2 for featureCounts.
Do I do the same for single end reads? I am confused whether there is a read 1 and read 2 for single end data, as I thought it was only read from one end? Would it then just be forward strand or -s 1 for single end data?