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Old 10-13-2014, 06:28 AM   #1
Location: Germany

Join Date: Dec 2013
Posts: 16
Default Calculating PSI values for rat RNA-seq


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!
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Old 10-08-2015, 11:13 PM   #2
Location: Singapore

Join Date: Oct 2009
Posts: 44

Hi kajot,

you can use this method that works with any annotation:
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