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 -----Original Message----- From: Luvina Guruvadoo [mailto:[email protected]] Sent: Tuesday, August 16, 2011 6:15 PM To: Diego F Pereira Cc: [email protected] Subject: Re: [Genome] Retrieving data from UCSC Hi Diego, In order to further assist you, may I ask what types of queries you are making in the Table Browser? If we have a better understanding of how you are using the Table Browser, it may be possible to download multiple annotations at once. Please email your reply to [email protected]. Regards, --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 8/16/2011 7:42 AM, Diego F Pereira wrote: > Dear all, > > I'm trying to analyze several non-coding SNPs. > > For this I would like to be able to analyze most of the information > regarding gene regulation that appears on the UCSC browser (DNaseI, > TFBSs, enhances, etc). > > For those annotations that have empirical support, it seems very > important to know the cell types/lineages in which the experiments were performed. > > Is really time consuming to download every single annotation by using > the Table Browser. > > By doing some research I found that probably Galaxy or kent source > tree may be of help. > > However I couldn't find a way for using Galaxy in this context, > neither a way to install kent source tree on a windows 7 x64 computer. > > I'm not a computer scientist, and the only code I know how to handle > is VBA for MSAccess. > > It seems a hard task to have to learn how to use Linux, MySQL AND > kent's packages just for this purpose. > > I will really appreciate if you can provide me with some guidance. > > Many thanks in advance, > > 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
