How to identify mRNA 3' UTR by bulk RNA-seq data

Question

[Ruixuan]

Hi there,

I was wondering if there are any tools that can identify mRNA 3' end and also 5' end by bulk RNA-seq data.

My goal is to determine the transcription start site and the transcription termination site.

I think maybe extracting mapping information from BAM file maybe an approach? But I'm not sure how to do with that.

Could you give me some advice?

Thanks in advance

[Amitm]

Hi, If your organism of interest has reference annotation available (like genome sequence and gene information in GTF format), then a transcriptome assembly followed by mapping, should give you genomic coordinates of 5' and 3' ends _as per your data.. when seen through prior knowledge of available annotation_ My experience is with mammalian genomes and aligners such as STAR or HISAT2, followed by StringTie would get you the answer.

[Ruixuan]

Thank you for your reply. But sadly there is no reference annotation for 5' and 3' UTRs, there is only CDS information. :(

[benformatics]

StringTie should still work for the assembly

Answer 1

[A. Domingues]

For the 3'UTR identification, I used isoscm in the past and was quite happy with the results. It will create a GTF with the 3'UTRs which you can use for further analysis. Mind you that this was done four years ago and better tools might exist.

[Ruixuan]

Thank you! I'll check it.