Good Morning Andrew: The version of the contig is not contained in the build specification. If you pick up this file: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/contigAgp.zip and unzip it, you will find column 1 of that file contains all the contig names used in the assembly. You can check that name list to see if any particular contig you are working with is in this build. For GRCh37/hg19, the naming scheme has changed completely. That build no longer uses names of the type NC_xxx
--Hiram ----- Original Message ----- From: "Andrew Yee" <[email protected]> To: "Vanessa Kirkup Swing" <[email protected]> Cc: [email protected] Sent: Friday, October 1, 2010 8:52:34 PM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] determine if a reference sequence is Hg18 v. Hg19 Thanks for the reply. If I enter NM_005656.2 with the .2 verson number with either hg18 or hg19 assemblies, no matches come up. I was wondering if you can specify a ref seq with the extension (even though NM_005656.2 is now defunct) have the Genome Browser return which build the ref seq is associated with? Thanks, Andrew On Thu, Sep 30, 2010 at 2:22 PM, Vanessa Kirkup Swing <[email protected]>wrote: > Hi Andrew, > > One of our engineers pointed out that you can also find a list for both the > hg18 and hg19 refseq names using our refgene table. An easy way to do this > is to use our table browser. > > To do this click on "Tables" from the blue navigation bar which will get > you to this page: http://genome.ucsc.edu/cgi-bin/hgTables > > Set the following: > clade: Mammal > genome: Human > assembly: hg18 or hg19 > group: Genes and Gene Prediction Tracks > track: RefSeq Genes > table: refgene > region: genome > output format: selected fields from primary and related tables > > Click on "get output" > > select "name" and other fields that might interest you. > > Click on "get output" > > Hope this helps. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ----- Original Message ----- > From: "Vanessa Kirkup Swing" <[email protected]> > To: "Andrew Yee" <[email protected]> > Cc: [email protected] > Sent: Thursday, September 30, 2010 10:04:50 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] determine if a reference sequence is Hg18 v. Hg19 > > Dear Andrew, > > The NCBI Reference Sequence NM_005656.2 is obsolete and therefore isn't > displayed anywhere on our browser. This sequence has been replaced in > genbank by version .3. > > Please feel free to contact the mailing list again if you have further > questions. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ----- Original Message ----- > From: "Andrew Yee" <[email protected]> > To: [email protected] > Sent: Wednesday, September 29, 2010 7:32:16 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] determine if a reference sequence is Hg18 v. Hg19 > > Is there a way to query a table to determine which Hg build a sequence > belongs to? For example, take NCBI Reference Sequence NM_005656.2 (see > also http://www.ncbi.nlm.nih.gov/nuccore/14602458). I believe this > sequence > is Hg18. Is there a way to directly determine this by querying a table in > the Genome Browser? > > Thanks, > Andrew _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
