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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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
