Question: Any tools to quantify intron retention in RNAseq data?
0
gravatar for lkmklsmn
3.5 years ago by
lkmklsmn720
United States
lkmklsmn720 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 • 3.2k views
ADD COMMENTlink modified 9 weeks ago by Chris_AI20 • written 3.5 years ago by lkmklsmn720
3
gravatar for Devon Ryan
3.5 years ago by
Devon Ryan73k
Freiburg, Germany
Devon Ryan73k 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 3.5 years ago by Devon Ryan73k

Astalavista software:

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

 

ADD REPLYlink written 3.1 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 3 months ago • written 3 months ago by Varun Gupta900
0
gravatar for Chris_AI
9 weeks ago by
Chris_AI20
Chris_AI20 wrote:

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

ADD COMMENTlink written 9 weeks ago by Chris_AI20
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