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 Post subject: Getting the regions back
PostPosted: Sun May 19, 2013 7:53 pm 
Dear GREAT team, thank you very much for your efforts providing the community with an excellent tool such as GREAT. During using it for ChipSeq analysis I was wondering if there is a way to retrieve the position of each region on their respective chromosome with the output somehow?
To make it more clear:
I entered my peaks in a bed file into GREAT, chose species assembly and sssociation rule settings, hit submit and then get a list of genes associated with my regions. Depending on the assoc. rule settings this list will not contain all regions from the initial bed file, only the ones I want, e.g. those close to the TSS for example.
In order to be able to use the resulting gene/region result in other applications, it would be useful that the genomic regions leading to identification of the associated gene could be preserved in the output.
Is this currently possible with GREAT?

Thank you very much!
Tobias
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 Post subject:
PostPosted: Thu May 30, 2013 11:09 am 
Site Admin
Hi Tobias,

You should be able to export the genomic regions that lead to a particular enrichment either by selecting the "All data as .tsv" option from the "Global Controls" drop down or "All ontology data as .tsv" option from the "Table controls" drop down for a particular ontology. The export file format at http://bejerano.stanford.edu/help/display/GREAT/Export outlines which column contains the regions of interest depending on the test you are performing.

Additionally, if you are interested in the pairwise association between genes and regions for an enriched term, you can click that particular term for its details page and expand "This term's genomic region-gene association tables" to get the association table.

You can also export all the genomic region and gene associations by "View all region-gene associations" from the "Global Controls" drop down. One this page the "Genomic region -> gene association table" table has all the regions in the input listed and regions that are not associated with genes are marked as "NONE".

Please let us know if you if you need anything else.

Thanks,
Bejerano Team
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