Sense and antisense transcripts identification

Question

[sukriti.gujarati]

I have generated reads from Direct RNA sequencing using Nanopore. Can someone guide me as to how can I separate the sense and antisense transcripts from the total reads generated? Further, I am specifically looking for methylation modifications in these S-AS transcripts.

Answer 1

[Istvan Albert]

If I recall it correctly the Nanopore direct RNA sequencing is strand specific so you can compare the mapping direction of the reads to the directionality of the annotations.

That way you can identify which read is sense and antisense.

If you did not have annotations the process would probably be a lot more complicated.