Operate on genomic intervals

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Operate on genomic intervals

Sarah
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



Reply | Threaded
Open this post in threaded view
|

Re: Operate on genomic intervals

Jen Hillman-Jackson
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
>
>
> ___________________________________________________________
> 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/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org