[miso-users] Exon-centric format

[Li, Robert]

Dear Dr Katz,

Thank you very much for your excellent work on MISO.
I am working on 2 groups of samples with 5 replicates: drug treated and  control.
The genome I am using is the Cow (ENSEMBL release 65.0). My reads are single-end (76 millions/sample).
I have successfully installed and run MISO (the latest version downloaded on 03/01/2012) using default parameters.
I managed to get Summary Output files for each of my samples.

It turns out my output files seem isoforms-centric.
What I really want to the exon-centric and am particularly interested in the modes of splicing events:
skipped exons (SE), alternative 3' UTRs (TandemUTR), and retained introns (RI).

My question  is: how can I get into the exon-centric mode?
Or
Which utilities do I use to extract information on those 3 types of splicing event?
Additionally, If I make a single BAM file for all my 10 samples for a group comparison, how do I code my sampleID?

Thank you very much for help in advance.

Rob Li, Ph.D.
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