Question: Any tools to quantify intron retention in RNAseq data?
0
gravatar for lkmklsmn
3.7 years ago by
lkmklsmn760
United States
lkmklsmn760 wrote:

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?

rna-seq retention intron R rnaseq • 3.4k views
ADD COMMENTlink modified 19 days ago by lhdcsu0 • written 3.7 years ago by lkmklsmn760
3
gravatar for Devon Ryan
3.7 years ago by
Devon Ryan75k
Freiburg, Germany
Devon Ryan75k wrote:

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.

ADD COMMENTlink written 3.7 years ago by Devon Ryan75k

Astalavista software:

http://genome.crg.es/astalavista/

 

ADD REPLYlink written 3.2 years ago by paulorapazote40

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?

ADD REPLYlink modified 5 months ago • written 5 months ago by Varun Gupta920
0
gravatar for Chris_AI
4 months ago by
Chris_AI20
Chris_AI20 wrote:

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

ADD COMMENTlink written 4 months ago by Chris_AI20
0
gravatar for lhdcsu
19 days ago by
lhdcsu0
lhdcsu0 wrote:

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

ADD COMMENTlink written 19 days ago by lhdcsu0

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

ADD REPLYlink written 14 days ago by Varun Gupta920
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