[miso-users] help

[Yarden Katz]

Hi Sudeep,

filter_events is only defined for two isoform events.  Filters like "delta psi" do not make sense alone when you have multiple isoforms (similarly for Bayes factor thresholds).  For example, you might consider an event significant if any of its isoforms have a delta psi value of at least X, etc.  Similarly, your coverage filters will need to apply to all/some/most isoforms, so there are many more ways to define such filters than in the simple two isoform case.  For multiple isoforms, you'll have to write your own filtering procedure by just parsing the *.miso_bf file, in the way that makes most sense for your analysis.

  --Yarden



On Jun 5, 2013, at 6:18 AM, sudeep dureja wrote:

> Dear MISO users,
> 
> Warm Greetings !!
> 
> I am Sudeep from India. Recently I have been working on alternative splicing. 
> My question is regarding extraction of genes which show more than two isoforms. 
> 
> Summary about my project: 
> 
> #1 Samples : 2 (case, control)
> #2 Generated BAM files using Tophat.
> #3 After comparison step, am stuck with filtering step. Error : More than two isoforms.
> 
> Please suggest me  parameters values (parameters; --bayes-factor, --delta-psi) and any way to use these file to get filter genes and sashimi plot.
> 
> Kind Regards,
> Sudeep
> _______________________________________________
> miso-users mailing list
> miso-users at mit.edu
> http://mailman.mit.edu/mailman/listinfo/miso-users