Hello Jianguang,

Junctions refer to known splice sites. TopHat has several options that work together to supply known junctions and to use them in various ways. This is used to direct splice identification. Given what you have explained about your experiment, I would not think this would be a desirable affect, so they are probably best left at default. Or, you could test to see the outcome. The parameter summary at the bottom of the tool form explains each and the manual can guide how to combine.


To do more research on this, the tophat.cuffli...@gmail.com mailing list is the definitive source, but there are plenty of prior discussion threads at seqanswer.com and other places. Try a search with "tophat junctions" or add in some of the parameter names to help filter through the results.

Best,

Jen
Galaxy team

On 8/15/12 1:24 PM, Du, Jianguang wrote:
Dear All,

I want to compare the pre-mRNA alternaive splicing events between
RNA-seq datasets. Should I use own junctions when I run Tophat? What
does "Own Junctions" mean?
Thanks.
Jianguang DU


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