Question: Identification of major isoform per gene from RNA-Seq
1
gravatar for Leszek
2.5 years ago by
Leszek3.8k
IIMCB, Poland
Leszek3.8k wrote:

I would like to find out whether there are any changes in major isoform (most expressed) per gene in my time course experiment. I can get this information by parsing FPKM values from cufflinks. 

Do you know of any more sophisticated tool/method capable of identifying major isoform changes between conditions? 

EDIT: I've ended up writing my own script. Details in here

EDIT2: fpkm2major.py can be downloaded from my github

 

rna-seq isoform major cufflinks • 1.6k views
ADD COMMENTlink modified 19 months ago • written 2.5 years ago by Leszek3.8k

Could you please share your scripts!

ADD REPLYlink written 19 months ago by Bionic0

Just to add on to this, you can try Kallisto -> Sleuth now to analyse at the transcript level, which was unavailable when this post started.

ADD REPLYlink written 19 months ago by andrew.j.skelton734.1k
0
gravatar for andrew.j.skelton73
2.5 years ago by
Newcastle Upon Tyne
andrew.j.skelton734.1k wrote:

I'd use CummerBund to extract your CuffDiff results into R, and get your gene FPKM and isoform FPKM tables. From that you'll need to map Gene ID's to Transcript ID's and filter each to find your dominant isoform. Beware that due to the nature of isoform switching, you may find that different isoforms are dominent in different conditions. I don't really see what you'll achieve by looking at only the "major isoforms". 

ADD COMMENTlink written 2.5 years ago by andrew.j.skelton734.1k

Isoform switching is exactly what I would like to analyse. If there is no tool for that, I'll write something myself. Thanks! 

ADD REPLYlink written 2.5 years ago by Leszek3.8k

Ah, I've done some work on that, but it's tricky to say the least. I used EBSeq with fractional counts, I'd suggest that'd be a good stating point. You can get fractional counts out of Tuxedo, using cummerbund, the function is hard to find - check out the repCountMatrix() function. 

 

ADD REPLYlink written 2.5 years ago by andrew.j.skelton734.1k

Thanks for advice. I've ended up writing my own script (fpkm2major.py) available also in my github

ADD REPLYlink modified 19 months ago • written 2.5 years ago by Leszek3.8k
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