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

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

rna-seq
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updated by A. Domingues A. Domingues • written by Ruixuan • Ruixuan

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.

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written by Amitm Amitm

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

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written by Ruixuan • Ruixuan

StringTie should still work for the assembly

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written by benformatics benformatics

1 answer

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.

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written by A. Domingues A. Domingues

Thank you! I'll check it.

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written by Ruixuan • Ruixuan

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