Hi Rene, Many of these tables are maintained at UCSC by their team of Genome Browser developers. These tables are updated constantly with corrected and enhanced annotations. For instance, CCDS related tables are freshened mostly on a weekly basis. You can easily upgrade your MapSNPs installation with the updated data for these tables by following MapSNPs installation instructions.
Other tables are provided as is, holding annotations data as published by the authors. They are unlikely to be updated unless original authors provide the updates. If you have any questions regarding MapSNPs tool please e-mail me directly. Best, Ivan On Monday, May 02, 2011 07:44:06 PM Lopez, Rene wrote: > Hi Brooke, > > Thanks a lot for you message. I'm looking to upgrade this tables/data > from hg18/36.1 to 36.3 > > >From the mapsnps installation file: > for hg18: > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ > ccdsGene > ccdsInfo > ccdsKgMap > chromInfo > kgAlias > kgProtAlias > kgSpAlias > kgXref > knownCanonical > knownGene > knownGeneMrna > knownGenePep > knownIsoforms > knownToEnsembl > knownToPfam > knownToRefSeq > refSeqSummary > snp130 > snp130CodingDbSnp > snp130Exceptions > snp130OrthoPt2Pa2Rm2 > > Those are from the mapsnps pipeline and it is also bundle with polyphen > 2 from Harvard as well. It uses those tables do translate to Amino > Acids, set the location to either exonic/intronic, etc... > > Does any of the files on the hg18/bigzips directory contains the data > for the tables above? > > Please let me know if this does makes sense, many thanks, > > Rene > > -----Original Message----- > From: Brooke Rhead [mailto:[email protected]] > Sent: Monday, May 02, 2011 6:23 PM > To: Lopez, Rene > Cc: [email protected] > Subject: Re: [Genome] hg18 36.3 (goldenPath) > > Hello Rene, > > Are you perhaps looking for the assembly files, located here? > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ > (We refer to this as the "Full data set" on our downloads page, here: > http://hgdownload.cse.ucsc.edu/downloads.html#human). > > NCBI's build 36.3 and 36.1 only differ in annotations, not in the > underlying genome assembly, so we do not have a Genome Browser for the > NCBI 36.3. > > Are you looking for a particular annotation track? > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > On 05/02/11 09:56, Lopez, Rene wrote: > > Dear Genome UCSC, > > > > > > > > I was wondering if you have the hg18 36.3 version available, I got > > what > > > is on (but I believe that is 36.1): > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ > > > Or if you know how to create those files for 36.3 version > > > > > > > > The currentGenomes directory is pointing to 37.1/2 > > > > > > > > Thanks in advance, > > > > > > > > Rene Lopez > > > > Bioinformatics Programmer Analyst III > > > > > > > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome -- Ivan Adzhubey, Ph.D. Instructor Genetics Division, Brigham & Women's Hospital Harvard Medical School HMS New Research Building, Room 0464C 77 Avenue Louis Pasteur Boston, MA 02115 tel.: (617) 525-4728 fax: (617) 525-4705 web: http://genetics.bwh.harvard.edu/genetics/members/Ivan_Adzhubey.html _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
