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. Thanks. Jianguang
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