Hello everyone,

I have to identify transcription start and end sites in a sequenced genome using rna-seq reads.

I have around 40 samples, for each sample start and end coordinate differs.

for example

sample1 read coverage starts from 1500 and ends at 1900

sample2 read coverage starts from 1600 and ends at 2000 etc. etc.

I was thinking about to use per base coverage but again it can drop in intronic regions.

Is there any tool/test that I can use to discriminate coverage drop between real start/end and everything else other than start/end(intronic region/sequencing error)

Thank you.