RNA-SEQ based transcription start and end site identification

Question

[rajeshkumar_vinod]

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.

[Phil S.]

something like this ?!?

[rajeshkumar_vinod]

thanks for the help,

i dont have to do it across species

[Manvendra Singh]

Wouldn't RABT assembly from cufflinks work in your case, you can further filter out transcripts of lower abundance, smaller length Hth

[rajeshkumar_vinod]

thanks for the help,

i will try to learn about RABT assembly