Are single-end reads processed the same as paired-end reads regarding strandedness?

Question

[sg197]

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?

Thanks!

Answer 1

[ATpoint]

It is the same except that you do not use the paired-end option (-p). The paired-end sequencing simply gives you additional information on the end of that fragment but it does not change anything towards R1 which is the one that is necessary for the strand information.