Calculating PSI values for rat RNA-seq

[kajot]

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!

[DerSeb]

Hi kajot,

you can use this method that works with any annotation:

http://onlinelibrary.wiley.com/doi/10.1002/0471142905.hg1116s87/abstract