Getting information about shortening or lengthening of UTRs from RNAseq data

Question

[Triple Nipple]

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

Answer 1

[mmfansler]

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 [[Article](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1415-3)] [[GitHub](https://github.com/zavolanlab/PAQR_KAPAC)]
• QAPA [[Article](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1414-4)] [[GitHub](https://github.com/morrislab/qapa)]

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

[darklings]

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...