Hi Rene, I'm sorry, I think I gave you incorrect information when I said that the only difference between NCBI's build 36.1 and 36.3 is in the annotations. That is the case for build 36.2:
http://www.ncbi.nlm.nih.gov/genome/guide/human/release_notes.html#36.2assembly "The genome assembly did not change with this update; it is identical to that provided for build 36.1." Build 36.3 is different: http://www.ncbi.nlm.nih.gov/genome/guide/human/release_notes.html#36.3assembly "This build adds the HuRef assembly and includes with no changes the reference genome assembly, the alternate Celera assembly, and partial chromosome alternate haplotypes." UCSC only hosts the reference genome assembly and partial chromosome alternate haplotypes (which are identical in hg18/36.1 and 36.3). We do not host the HuRef or Celera alternate assemblies. Therefore, we have not made any changes to the tables you list based on NCBI's build 36.3. However, you should be aware that some of those tables are updated nightly by an automatic process (the ccds* tables), and some are updated periodically when we release a new version of the UCSC Genes track (the knownGene* and kg* tables). -- Brooke Rhead UCSC Genome Bioinformatics Group On 05/02/11 16:44, 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
