I have made new transcript isoforms using Cufflinks and I would like to know what splicing events made particular isoforms when a gene makes more than one isoform. i.e., does an isoform contain a retained intron or alt 3' SS. Each isoform could have more than one annotation.
I am sure there must be a program out there that can do this but I am not sure which to use. At the end of it I want to know what AS types are the most common in this genome and which are the most common in transcript isoforms that are differential between treatments.
I thought PASA or SplicingTypesAnno or something else might help but so far it is not clear to me that they can take a Cufflinks GTF and then annotate the isoforms with splicing events. Any advice which program to use, how to use it and what the output will actually look like would be amazing!
I think AStalavista can do it easily but the output is so far confusing. It does not seem to give me what I want.
Ah great, thanks for the advice (and letting me know I am not the only one out there not liking ASalavista). Suppa definitely looks good to use, I look forward to trying it out. I have heard elsewhere that PASA might be able to do what I want if I give it a dummy fasta file and accept it will rename my
transcript_IDs. They said they might work on a new standalone version of it that will just take a GTF as input to give annotations to transcript isoforms, which would be great as I love their annotation system for splicing.