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 Técnico
Portugal
tel: +351 218417233
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Jennifer Hillman-Jackson
Galaxy Support and Training
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