Hello Yang Yang, You can find a description of what the casing means for different download files here:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ For #2 you can get the data one of two ways - via the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) or from the downloads page. If you go to the Table Browser page after selecting hg19 you can select the group "Genes and Gene Prediction Tracks". This will then allow you to chose a gene prediction track and table (i.e. UCSC genes, knownGene table) to download. If you're not sure which tables you want to access, you can also click on "describe table schema" for any table and it will take you to a description of that table's contents. If you only want to retrieve certain columns from a given table you can also select: output format: "selected fields from primary and related tables" Once you click on "get output" this will take you to a menu where you can specify which fields you want to retrieve from your tables of interest. If you find a table and want to download the whole thing (without excluding any columns) you can also find it in the downloads section here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ (i.e. for the knownGenes table you would download one of these files: knownGene.sql, knownGene.txt.gz) Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 03/08/11 18:10, yang yang wrote: > Hi Dear, > > I'm Yang Yang ,a graduate student in Southeast University in > Nanjing,China.Now I use UCSC to analyse data of ChIP-Seq only for scientific > research.I have two questions to consult: > > 1 what meanings are the capital letters and the lower case letters in the > chromosome sequece of hg19 ? > > 2 I want to to build our database in our server,so we need the information > of annotation for all chromosomes in human,including:gene > name,promotor,intron,exon,location in the chromosome,and so on.What document > should I download from the page of annotation database ? > > Best regards, > Yours sincerely, > Yang Yang > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
