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Question: Use Own Junctions Or Not
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gravatar for Du, Jianguang
6.3 years ago by
Du, Jianguang • 380
Du, Jianguang • 380 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
rna-seq tophat • 811 views
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modified 6.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.3 years ago by Du, Jianguang • 380
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gravatar for Jennifer Hillman Jackson
6.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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.cufflinks@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 -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k
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