Hi Sandra,

Galaxy can certainly be used to correlate a set of unknown genomic coordinates with another annotated set of genomic corrdinates, such as those available from UCSC, Biomart, etc.


The tool set to look at is "Operate on genomic intervals" and an example of how these tools are used, in particular the "Join" tool, can be found in several tutorials. Among these are:

https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
-> Protocol1 shows a general overview of how to join two datasets and merge back any lost information -> Protocol3 has datasets available for practice analysis: ChIP-seq result and a promoter dataset

https://main.g2.bx.psu.edu/u/aun1/p/galaxy101
-> Similar to Protocol1 (above) in many parts, but includes a workflow creation step that you may find helpful to know about.

http://wiki.galaxyproject.org/Learn#Other_Tutorials
-> " Analysis of ChIP-seq data in Galaxy" for an exact example of filtering and interval comparison with RefSeq -> " Using the UCSC Genome Browser and Galaxy to study regulatory sequence evolution in Drosophila" for an example of how to intersect data directly in the UCSC Table browser, then export to Galaxy. Any BED file in Galaxy can be sent to UCSC as a custom track.

Best,

Jen
Galaxy team

On 3/25/13 4:17 AM, Sandra Santos wrote:
Hi

My name is Sandra and I'm a curator of a database of transcriptional relationships in yeast. We are doing our annual update, and in one paper I found a number of ChIP-seq results. Unfortunately, the authors only included in the supplemental information the genome coordinates, but no information regarding what the binding position corresponds to (promoter, ORF...). When I asked the authors for this information, they told me to do it myself. I'm actually quite busy and don't have time to waste analysing their results, but decided to check if GALAXY has a tool where I can use this list of positions as an input and get the annotation of the region.

Thanks for your help

--
Sandra C. dos Santos, PhD
Post-Doctoral fellow
https://fenix.ist.utl.pt:443/homepage/ist146260 <https://fenix.ist.utl.pt/homepage/ist146260>
Biological Sciences Research Group
Instituto Superior T├ęcnico
Portugal
tel: +351 218417233














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