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

    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!

  • #2
    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.

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    • #3
      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";

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