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.