Thank you very much Vanessa! I'll try your links in short. I would like to ask, since the UCSC browser already displays the information graphically, have you already think about displaying the same type of information in a tabular way? I think that will be kind of easy for you to do, and of great help for non-linux-programmer researchers. Anyway this is just an idea. Thank you again for the information. Keep with the good job. Kind Regards, Diego
-----Original Message----- From: Vanessa Kirkup Swing [mailto:[email protected]] Sent: Friday, August 19, 2011 5:30 PM To: Diego F Pereira Cc: Jeff Murray; [email protected] Subject: Re: [Genome] Retrieving data from UCSC Hi Diego, We've tried to present our data in a way that is useful for non-programmers, but the in-depth research that you are trying accomplish requires a bioinformatics background. This means there is no easy way to get all the data using the table browser. We suggest that you take a look at the links below to learn the various ways to access the data that is displayed on our site. Open Helix Tutorials: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28 Downloads: http://hgdownload.cse.ucsc.edu/downloads.html ENCODE Downloads: http://genome.ucsc.edu/ENCODE/downloads.html Direct MySQL access to data: http://genome.ucsc.edu/FAQ/FAQdownloads#download29 We hope this information is useful. If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Diego F Pereira <[email protected]> Date: Thu, Aug 18, 2011 at 2:13 PM Subject: Re: [Genome] Retrieving data from UCSC To: [email protected] Cc: Jeff Murray <[email protected]>, [email protected] Thank you Pauline for your response, Since non-coding SNPs can affect different elements depending upon the cell type, tissue and time of development, I need to be able to get the most of the information the UCSC browser offers organized in a table manner for further comparisons. The tracks I'm interested in, are: Mapping and Sequencing Tracks: -BU Orchid (v1 and v2) -GC percent -Recomb Rate -Mapability -GRC patch release Phenotype and Disease Associations Tracks: -GAD View -RGD Human QTL -Decipher -OMIM Genes -OMIM Pheno Loci -GWAS Catalog Genes and Gene Prediction Tracks: -All tracks mRNA and EST Tracks: -All tracks Expression: -All tracks Regulation: -All tracks As I said, I would like to be able to retrieve all this information with their respective scores, cell information (when applicable), signal values, etc. into tables. In this way I hope we can improve the decision making process for the experiments needed to be conducted based upon the results of preliminary data. I think to be able to get all this information with their supportive evidence in tables is of the most importance for researchers who perform SNP analyzes. In this way we can take better decisions, formulate better hypotheses and get the most UCSC browser offers. Kind Regards, Diego -----Original Message----- From: Pauline Fujita [mailto:[email protected]] Sent: Thursday, August 18, 2011 3:00 PM To: Diego F Pereira Cc: [email protected] Subject: Re: [Genome] Retrieving data from UCSC Hello Diego, You may find this page about cell types to be a useful starting point for your queries: http://genome.ucsc.edu/ENCODE/cellTypes.html To assist you further in finding additional data we would need to know exactly what data you are looking for and from which tracks. If you can provide specific examples of the data/tracks you need for some example SNPs we might be able to help you to construct appropriate Table Browser queries. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 8/17/11 4:18 PM, Diego F Pereira wrote: > Thank you Luvina and Sean, > > What I really would like to do is to be able to have in a single table > all the annotations displayed in the Genome Browser for multiple SNPs, > with all their detailed information (i.e. Signal values, scores, cell > information etc). > > It would be great if I can do that in a single step, but I don't think > that is possible (hopefully I'm wrong). > > If this is not possible right now, at least I would like to be able to > download this information for each SNP at the time. > > > > Now, regarding the way I'm using the Table Browser, I'm picking every > single track in order to get the information. > > Since I'm interested in the Sex and Age of the people from whom cell > lines were derived and the lineage and tissue from where the samples > were taken, what I'm actually doing is to click on the cell type > reported for every experiment to get the more complete information. > > This way works, but it is really painful! > > I didn't find a way to query multiple tracks at once from the Table > Browser neither a tutorial to use Galaxy for this purpose. > > The best starting information I found was a paper by Peter Schattner > (Automated Querying of Genome Databases, 2007). > > > > Thank you for your interest and help. > > > > All the best, > > Diego > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
