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How to get the 3'UTR for genes in my gff file based on transcriptome?

I have a gff file with CDS regions of all genes registered. Now I have some RNA-seq data that I have mapped to the reference genome using hisat2. What I hope to do is to find the UTR region for all genes in gff.

I hope to first assemble a transcriptome using stringtie, then I should be able to get the UTR since they should be the extended 3' sequence in the transcripts that are not covered by CDS right? Is this plan feasible? What software I can use to extract the UTR part from the assembled transcript for all genes in my gff file?

stringtie assembly rna-seq transcriptome
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written by tianshenbio tianshenbio

Please add some details, how did you generate the gff file and what is the organism, if its a model organism then just retrieve the UTRs from biomart. According to what you have posted you want to extract regions which are not present in the gff file, This can be done using bedtools intersect after some format conversions.

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written by ashish ashish

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