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Question: Operate On Genomic Intervals
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gravatar for Sarah
7.1 years ago by
Sarah • 20
Sarah • 20 wrote:
Hi All, I have two files containing multiple scaffolds and their genomic intervals. Now I want to substract the intervals of one file from the other, but apparently this tool is only available if all the data in the chromosome column have the same name. Does anybody known a way how to handle files with different names in the chromosome column? Thanks a lot in advance, Sarah
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modified 7.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.1 years ago by Sarah • 20
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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:
Hi Sarah, If you just want to compare rows between two files without interpreting genome positional information (similar to the unix "comm" command), then please see the tools under "Join, Subtract and Group". In particular, "Subtract Whole Dataset", but perhaps also "Compare two Datasets". You will likely need to convert the datatype to be "tabular" before using the "Compare" function. Do this by using the "Edit Attributes -> Change data type" form, located by click on the pencil icon in the top right corner of a dataset's box in the history panel. The instructions in the "Compare" tool form state to use "Text Manipulation->Convert", but if your file is already in interval format, a specific type of tabular data, then this is not an appropriate (or needed) step. 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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