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  • Calculating PSI values for rat RNA-seq

    Hi,


    could someone recommend me something to calculate Percent Spliced-In (PSI) values for all the exons of rat in a paired-end RNA-seq experiment ?

    I tried out MISO, but it seems to me that for exon-centric table of PSI values you have to provide it with a table of splicing events which AFAIK doesn't exist for rat.

    I would love to use something simple that would base only on given RNA-seq run + official gene annotation like Ensembl.

    Any ideas ? Thanks!

  • #2
    Hi kajot,

    you can use this method that works with any annotation:

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