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Any tools to quantify intron retention in RNAseq data?

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?

r rna-seq rnaseq intron retention
• 8,381 views • link
updated by Ram Ram • written by lkmklsmn lkmklsmn

3 answers

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.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

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?

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updated by Ram Ram • written by Varun Gupta Varun Gupta

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

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written by ResearchR ResearchR

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

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written by lhdcsu • lhdcsu

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

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written by Varun Gupta Varun Gupta

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

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written by lhdcsu • lhdcsu

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