Paired-end data?

[anastasiaprime]

Hello

Does pipeline work with paired-end data? Or only SE?

[bounlu]

It currently works with SE data only. I suggest to merge PE reads with a tool like NGmerge or fastq-join and then run the pipeline with the merged reads.

[apeltzer]

I would even suggest to only use R1 and ditch R2 entirely. It's small rna and thus covered by your R1 in its entirety ... no need to merge anything there.

[bounlu]

It depends on your read length and the small RNA species you are looking for. If you have PE50 or even PE75 and you want to quantify tRNA, snRNA, snoRNA, etc., then you better use both reads. If you are only interested in miRNAs, then R1 would be sufficient.

[anastasiaprime]

Thank you @apeltzer @bounlu , I appreciate that!
Indeed, I am processing microRNA data, but I have paired 50 bp reads from the lab. And it seems to me that there is no microRNA in the reverse (R2) reads at all, so I will work only with R1.