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Question: Bed To Wiggle?
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gravatar for shamsher jagat
7.1 years ago by
shamsher jagat • 590
United States
shamsher jagat • 590 wrote:
Is there an option to convert Bed file to wiggle file in Galaxy? Thanks
galaxy • 2.0k views
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modified 7.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.1 years ago by shamsher jagat • 590
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gravatar for Jennifer Hillman Jackson
7.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello, Galaxy does not have any specific tool to do this conversion, as it is generally not an efficient conversion. Converting to bigBed and altering display attributes is usually better (if graphing/visualization is the goal). That said, the UCSC Genome Browser group (the original author for both of these datatypes) has some help for converting that you can explore, including some simple shell scripts to convert formats in batch. The warning are worth understanding, since a file that is too large to visualize (at all or in a meaningful way) is easy to create. Starting place link: http://genomewiki.ucsc.edu/index.php/Wiggle_BED_to_variableStep_format _conversion If you or anyone else reading this post were to create a wrapped tool for Galaxy that converts a BED file to a fixed-step wiggle (with some appropriate limits to avoid the problems explained on the UCSC wiki), it would be welcomed in the Tool Shed: http://wiki.g2.bx.psu.edu/Tool%20Shed Hopefully this helps! Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
ADD COMMENT • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k
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