Any tools to quantify intron retention in RNAseq data?

Question

[lkmklsmn]

Hi biostars,

I am looking for an established tool to quantify intron retention in RNAseq data. I have come across spliceR package but its seems to be rather difficult with non-cuffdiff generated data.

Any ideas?

Answer 1

[Devon Ryan]

This can be done with DEXSeq, for which one needs to simply tweak an annotation file a bit. Both Alejandro Reyes and I give example scripts for the conversion in this thread on seqanswers. You may also want to read through the "Detecting differential usage of introns from RNA-seq daasets" on the bioconductor email list.

[paulorapazote]

Astalavista software

[Varun Gupta]

Hi Devon,

I am trying to run your script on seqanswer. With hg19.gff(generated from DEXSeq python scripts), I am using import.gff2 as per your command but

1. It does not use asRangedData=F
2. Also it gives warnings as closing unused connection 4 (Homo_changed_37.74.gff) after I remove asRangeData=F

At the step

with_introns <- endoapply(grl, add_introns)

the code is still running and is taking a lot of time. Is this normal?

Answer 2

[ResearchR]

Try this: https://github.com/williamritchie/IRFinder

Answer 3

[lhdcsu]

Use iREAD (intron retention analysis and detector) specifically designed to quantify intron retention: http://www.genemine.org/iread.php

[Varun Gupta]

Reads in the Bam file created should be mapped to the transcriptome or whole genome??

[lhdcsu]

whole genome. (tested on BAM from the STAR software)