Hi Katrina, Right now I'm using BED detail with itemRgb as I was able to find searching in the mailing list and you kindly point me to, but in order to use this I had to come up with a script to put the right r,g,b color code depending on the function my SNP software is calling, or if the software gives a rsID I just grab the function from snp132 track. But this was cumbersome and I'm not getting present and future extras from "Personal Genome SNP format". So even if there is not an option to change the color scheme, I would like to host my SNPs track in this format.
I tried to look for pgSnp type in: src/hg/makeDb/trackDb/README There is not such a thing and I couldn't find any other type I could think is the correct one to put in my "trackDb.ra" file. This website you comment and I already checked: http://genome.cse.ucsc.edu/FAQ/FAQformat.html#format10 Only talks about custom tracks not local tracks which is what I would like to use, I also couldn't find the right utility to load the table into the database(like hgLoadBed). If you could point me to a documentation to use pgSnp type track as a local track I would highly appreciated it. Thank you very much for your help. PS: Should I ask this type of question at [email protected]? PPS: Would it be better to adjust the reply-to of the list to the list address, I keep forgetting to use reply-all. -- Carlos Borroto Baltimore, MD On Mon, Apr 25, 2011 at 5:21 PM, Katrina Learned <[email protected]> wrote: > Hi Carlos, > > For directions on loading your own track into your mirror see: > http://genomewiki.ucsc.edu/index.php/Adding_New_Tracks_to_a_browser_installation > Additionally, the "See Also" section of that page, which provides more > helpful resources: "For a generic discussion of how to load any type of > track into your local browser mirror, refer to the document in the source > tree src/product/README.trackDb and the discussion of how the trackDb > entries function in src/hg/makeDb/trackDb/README". > > The Personal Genome SNP would probably work best for your purposes, however > the colors displayed cannot be based on a SNP's function. In order to color > the track in this way, you would have to use a BED detail format, which > wouldn't automatically calculate all that the Personal Genome SNP format > does. For more information about these track types, see this previously > answered Mailing List question: > https://lists.soe.ucsc.edu/pipermail/genome/2011-February/025155.html > > Please contact the mail list ([email protected]) again if you have any > further questions. > > Katrina Learned > UCSC Genome Bioinformatics Group > Carlos Javier Borroto wrote, On 04/22/11 13:50: >> >> Hi, >> >> Is it possible to create a "Personal Genome SNP" local track(not just >> a custom) in a local mirror? What track type can I use? >> >> Also, I see the "Personal Genome SNP" custom track detail page gives >> information about the function of the SNP, but can this information be >> shown using a color code like in snp132 instead of the allele >> frequency coloring? >> >> Thanks, >> -- >> Carlos Borroto >> Baltimore, MD >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
