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  • xhuister
    replied
    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";

    Leave a comment:


  • dpryan
    replied
    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.

    Leave a comment:


  • 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!

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  • seqadmin
    Recent Advances in Sequencing Analysis Tools
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    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
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