I'm looking for a program that will take a GTF/GFF3 file as input and produce a report describing the observed alternative splicing events (skipped exons, retained introns, mutually exclusive exons, etc). Honestly, it seems like a very straightforward task to write such a program/script, and I was planning on doing so myself. Before writing the code, however, I thought I would make sure that nobody else has shared code for doing this type of task before.
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Daniel Standage
Hi Daniel,
How about your work on this topic going on?
I have found there are two package worked for this purpose, i.e alternative splicing event classification.
Running Cuffcompare
Cufflinks includes a program that you can use to help analyze the transfrags you assemble. The program cuffcompare helps you: Compare your assembled transcripts to a reference annotation Track Cufflinks transcripts across multiple experiments (e.g. across a time course) From the command line, run cuffcompare as follows: cuffcompare [options]* <cuff1.gtf> [cuff2.gtf] ... [cuffN.gtf]
Cuffcompare should do this.
Two comments: first, cuffcompare is for comparison of two or more GTF files (not shocking given its name), whereas I am looking for something that will take a single annotation file; second, it's not clear to me where in the cuffcompare output I will find a summary of alternative splicing events. Perhaps you can clarify.
I'm working with an organism that has no reference annotation. I can use TopHat/Cufflinks to align the RNA-seq reads and assemble the alignments into transcripts. In cases of alternative splicing, a single Cufflinks-produced GTF file will contain multiple overlapping transcript annotations sharing some but not all exons. Alternatively, I can use some gene annotation workflow to produce transcript annotations. Depending on the evidence I provide, this may also identify distinct transcripts that share some but not all exons.
In either case, I don't need to compare a GTF/GFF3 file to another file to identify alternative splicing events, I just need to look for transcripts that share some (but not all) exons. Am I missing something here?
You could be right, I'm just not aware of how to go about finding alternative splicing events for non-model organisms without a consensus reference to compare to.
If I had to take a crack I'd probably consider the transcript with highest abundance as the reference transcript and annotate alternative splicing events by comparing the rest to to it. That's just my guess.
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I was also interested in such a program. Have you found anything or would you care to share what you developed?
I am now looking for the same thing. To take a Cufflinks GTF and annotate each transcript with splicing type. Why is this so hard?
did you find anything for plants?..
Yes I found SUPPA. It worked well. It is a set of python scripts and the generateEvents script is what you want to run on the GTF from Cufflinks/Cuffmerge and then the output files called .ioe have the events.