[miso-users] Unannotated SE events and multi-mapping reads

[Sahin Naqvi]

Hi,

I have two questions about MISO:

1) I'm interested in quantifying the PSIs of the exons of a few genes of interest, and have noticed that the annotated skipped exon events only contain a fraction of the possible skipped exon events (which makes sense given that they are from existing annotations). How would MISO deal with reads that were consistent with some other SE event? If it ignores that, is there a way for me to manually add potential events to the alternative event annotations?

2) How does MISo deal with multi-mapping reads when quantifying PSI values? Is it similar to the cufflinks method?

Thanks,
Sahin Naqvi
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