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Question: TopHat: Raw junction and juncs files
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gravatar for madkisson
3.3 years ago by
madkisson • 30
United States
madkisson • 30 wrote:

Hi

I'm having a hard time finding information on what exactly the advantage of using the Raw Junction option in TopHat would be. Mostly people just cut and paste the explanation from the TopHat manual. Am I wrong in believing that all this does is take information from one TopHat run and make future runs a little quicker and easier? If that's the case I'm in, but where can I find the BED_to_juncs tool? Doesn't show up in the Tool Shed.

Thanks

Michael
tophat .juncs file junctions • 1.0k views
ADD COMMENT • link •
modified 3.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.3 years ago by madkisson • 30
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gravatar for Jennifer Hillman Jackson
3.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Using a junctions file introduces those splice sites into your analysis. This can be advantageous when those additional splices are not contained in your sample data but are needed for the experiment. These junctions can be from known transcripts, prior analysis, etc. Using this type of data does not mean that the tool will run quicker.

Junctions can be supplied in text format (the tool you mention is not necessarily needed). The tool form and manual have the specifications for the file format. 

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k
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