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

On 10/28/11 8:19 AM, Sarah 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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