Getting information about shortening or lengthening of UTRs from RNAseq data
1
0
Entering edit mode
2.6 years ago

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 • 510 views
ADD COMMENT
1
Entering edit mode
2.6 years ago
mmfansler ▴ 410

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.

ADD COMMENT
0
Entering edit mode

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...

ADD REPLY

Login before adding your answer.

Traffic: 1063 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6