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Question: Bed To Bigbed Conversion
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gravatar for Gijs Santen
7.5 years ago by
Gijs Santen • 20
Gijs Santen • 20 wrote:
Dear users, I am only recently beginning to discover Galaxy, so please bear with me... I am trying to convert a bed to bigbed file, but the job remains 'grey', it does not start. I repeated the same conversion with the UCSC sample file (http://genome.ucsc.edu/goldenPath/help/examples/bedExample.txt) , but it still does not work. I simply uploaded the file directly from the link and then used the bed-to-bigbed conversion tool. So either I am doing something wrong or could there be an issue with this conversion on the server? Thanks for your insights, Gijs
galaxy • 1.6k views
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modified 7.5 years ago by Kanwei Li • 270 • written 7.5 years ago by Gijs Santen • 20
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gravatar for Kanwei Li
7.5 years ago by
Kanwei Li • 270
Kanwei Li • 270 wrote:
Hi Gijs, We only have one node on our main instasnce to do these bigBed and bigWig conversions since they take so much memory, so it may be queued for a while. Thanks, K
ADD COMMENT • link written 7.5 years ago by Kanwei Li • 270
Hi Kanwei, thanks for your reply. I will leave them in the queue. I also did several bigwig conversions and these were executed directly, so I did not think this was an issue. I'll wait and see, Gijs
ADD REPLY • link written 7.4 years ago by Gijs Santen • 20
FYI: The bedToBigBed converter is one of the lower memory usage big* converters, with a longer running time: http://genomewiki.ucsc.edu/index.php/Big_file_converters --Hiram
ADD REPLY • link written 7.5 years ago by Hiram Clawson • 260
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