Hi,

I have bacterial RNA-seq data from paired-end reads (2x75). I'm interested in sense/antisense differential expression.

I would like to know if makes sense to merge R1 and R2 into one read (if overlaps) or maybe work only with 75 bp reads (R2 ones).

Thanks, Bernardo
<p>Why bother? Presuming that you used a stranded protocol when making the libraries, you can just align things as pairs and tell whichever program you use to do counting to observe strandedness of pairs. Both htseq-count and featureCounts can do that.</p>

<p>To get at the antisense transcription, one could just run the counters again and just tell them to use the other read as the strand reference (e.g., running <code>htseq-count -s yes ...</code> and then <code>htseq-count -s reverse ...</code>).</p>
