Dear All,

I have two more questions about settings for Tophat.

My aim is to look for the defferential splicing events between cell types.

After I checked "Use Own Junctions", three more options came out:

1) "Use Gene Annotation Model"

2) "Use raw Junctions"

3) "Only look for supplied junctions"

As instructed by Jen, I checked "Use Gene Annotation Model", and input iGenome 
mm9 genes.gtf as "Gene Model Annotations".

However, I am not sure if I should choose to "Use raw junctions" and "only look 
for supplied junctions". Please help me set up these two options.



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