Hello,
In HTSeq's manual for the stranded parameter, they state:
"For stranded=no, a read is considered overlapping with a feature regardless of whether it is mapped to the same or the opposite strand as the feature. For stranded=yes and single-end reads, the read has to be mapped to the same strand as the feature. For paired-end reads, the first read has to be on the same strand and the second read on the opposite strand. For stranded=reverse, these rules are reversed."
I interpreted the line " For stranded=yes and single-end reads, the read has to be mapped to the same strand as the feature." as meaning single-end data only needs the stranded=yes parameter whether it is reverse or not. Is this interpretation correct, or should I be using stranded=reverse for single-end data also if it is in fact reverse? The wording here is slightly confusing, since they only mention the reverse option after talking about paired-end data.
I usually work with paired-end data and am currently working on a small project involving single-end data, so my apologies if this seems like a simple question.
Thank you in advance to anyone who can help with this.
