Hello, As stated on the Rat gateway page, the June 2003 rat (/Rattus norvegicus/) genome assembly is based on version 3.1 produced by the Atlas group at Baylor Human Genome Sequencing Center <http://hgsc.bcm.tmc.edu/> (HGSC) as part of the Rat Genome Sequencing Consortium. The data was not assembled at UCSC. Please see the credits linked from the gateway for additional contributors.
One immediate option for you is to ftp the data from NCBI, format as necessary, and upload the result as a custom track. Or just use the data in flat file format if that is more useful for you. You request will also be forwarded to our development team for consideration (create rn4 Contig Map track). Thank you for the data suggestion, Jennifer Jackson UCSC Genome Bioinformatics Group Wenwu Cui wrote: > Dear Sir/Madam: > > > > Now that there is contig map provided by NCBI > (ftp://ftp.ncbi.nlm.nih.gov/genomes/MapView/Rattus_norvegicus/sequence/current/initial_release/seq_contig.md.gz) > for rn4, I would like to know how those chrN_random(s) are assembled at > UCSC. There is no result returned by searching a rat contig in Genome > Browser. I am wondering when the rat ctgPos.txt file will be available. > > > > Thanks! > > > > Wenwu Cui > > NextBio > > > > >> Hello Xiaomin, >> > > > > >> The ctgPos tables, which correspond to the "Map Contigs" tracks on the >> > > >> human and mouse assemblies in the Genome Browser, is based on data >> > > >> provided by NCBI. There is no "Map Contigs" track for the rat (rn4) >> > > >> assembly, which was produced by the Atlas group at Baylor Human Genome >> > > >> Sequencing Center (HGSC). >> > > > > >> -- >> > > >> Brooke Rhead >> > > >> UCSC Genome Bioinformatics Group >> > > > > >> Xiaomin Ying wrote: >> > > >>> Dear UCSC colleagues, >>> > > > > >>> I couldn't find the file ctgPos.txt.gz from the rn4 database >>> > > http://hgdownload.cse.ucsc.edu/goldenPath/rn4/database/ which is > > available for all other tracks. Could you please check? Thanks. > > >>> Xiaomin >>> > > >>> _______________________________________________ >>> > > >>> Genome maillist - Genome at >>> soe.ucsc.edu<http://www.soe.ucsc.edu/mailman/listinfo/genome> >>> > > >>> http://www.soe.ucsc.edu/mailman/listinfo/genome >>> > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
