Tools for detecting Alternative Splicing events from a GFF/GTF annotation file?

[xhuister]

Hi all,

I'm looking for a program that will take a GTF/GFF file as input and produce a report describing the observed alternative splicing events (skipped exons, retained introns, mutually exclusive exons, etc).

An example output like this:
alt_acceptor chr1 + 35633 35634
alt_acceptor chr1 + 35639 35640
retained_exon chr1 + 35448 35498
skipped_exon chr1 + 35448 35498


(A same thread was proposed by other people but no solution: https://www.biostars.org/p/95565/ )


The tool PASA (http://pasa.sourceforge.net/) can generate the AS list I need, but it does not take the gff/gtf as input.

Is there an easy-to-use tool for this purpose? Thank you!

[dpryan]

This shouldn't be too terrible to write in R using GenomicRanges. GTF files are nicely formatted, so you'd just read it in, split it by Gene ID, and then apply a function (you'd have to write it) to analyze each gene. This would take some thought to do properly, but should be doable by a non-bioinformatician.

[xhuister]

After my post, I found that astalavista (http://genome.crg.es/astalavista/FAQ.html) can be a good choice for me. It can read a gff annotation file and output AS events like:
Chr4 as_event 8055242 8055378 . + . as_code "1^2- , 0";
Chr4 as_event 8056139 8056707 . + . as_code "1^2- , 0";