Re: [galaxy-user] defining regions

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Re: [galaxy-user] defining regions

Guruprasad Ananda
Hello Amit,

You can do this as follows:
1. Go to 'Get data > UCSC main' tool and select "Genes and gene predictions" track, specify your chr/region of interest, check 'output to Galaxy' box and hit 'get output'. In the next page, select 'exons' and run the tool.
2. The output of step (1) will result in a list of exons residing in the region of interest. Now you can use "Operate on genomic intervals > Join" tool to obtain a list of CHIP signals overlapping with exons.
You can do the same for introns, by selecting 'introns' in step (1).

Hope this answers your question.
Thanks,
Guru.

On May 18, 2010, at 1:57 AM, research pal wrote:


Dear Galaxy,
                      First of all let me thank you people for the effort that you are involved in to help the bench scientists world over.
I have the ChIP data from ENCODE and I want to see from which part i.e. Exon,Intron or intergenic regions of the human genome they are derived from.In this case can the tools available at galaxy or genome browser help me to reduce my manual efforts ?

warm regards,
Amit.

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