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Old 10-07-2013, 11:12 AM   #1
mcgreevy
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Default Bedtools partition

I'm attempting to get the depth of coverage for regions of a genome out of a bed file. Essentially the reads overlap and are large and small and I want a file with each segment broken up and the coverage calculated. I haven't been able to achieve this using bedops partition function, does anyone have any ideas?
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Old 10-07-2013, 11:22 AM   #2
GenoMax
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Bedtools and Bedops are two separate packages. Which of the two are you referring to since both have functions to calculate stats: http://bedtools.readthedocs.org/en/l...genomecov.html or https://bedops.readthedocs.org/en/la...cs/bedmap.html
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Old 10-11-2013, 06:17 AM   #3
mcgreevy
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Thanks the error was in the version of bedops. partition does not seem to work on my computer in the new v3. The same script worked on another computer with an older versions. Cheers for the response.
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