Sorry for bothering you, but I am not sure if there is a standard protocol for inferring or detecting transcriptional start sites (TSS) from bacterial RNA-Seq paired-end data, and I would be very grateful if someone could help me here. I have been searching and I am not really sure what to do! :)
The data is already mapped vs the reference genome using the gtf annotation file. I just want to determinate the +1 for the different transcripts! Is that as easy as taking the first nucleotide of each operon? Or is there a better way?
I am quite lost, and I would really appreciate any help. Thank you very much.