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

On 11/4/11 3:43 PM, shamsher jagat wrote:
Is there an option to convert Bed file to wiggle file in Galaxy?

Thanks


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