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Getting information about shortening or lengthening of UTRs from RNAseq data

How can I get information about the length of UTR sequence from RNAseq data that aligned to reference? I need to know for each transcript if the 3UTR got longer or shorter. Is this possible?

Note: In the ensembl .gtf file the UTRs were annotated, I managed to find their expression, but can I get info whether they got shorter or longer?

Thanks

rna-seq rna-seq assembly
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updated by mmfansler mmfansler • written by Triple Nipple • Triple Nipple

1 answer

There are quite a few different methods in the field.

While Ensembl has been continuously improving their annotations of 3' UTRs, it is definitely not comprehensive. However, there have been two recent bulk RNA-seq-based 3' UTR quantification tools that include the ability to supplement annotations with evidence from cleavage sites databases. These are

PAQR takes BAM as input; QAPA will start from FASTQ and use Salmon to run the quantification.

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written by mmfansler mmfansler

Some other tools first identify de novo APA sites from RNA-seq and then test which genes have shortening or lengthening UTRs. I tried QAPA and another labmate tried DaPars, and the results are quite different...

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written by darklings darklings

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