Hello Sho, There are two basic methods:
1) Use the Table browser to do this. Select the Genbank assembly/track of interest, use the "identifiers" filter to limit the output, and select output "selected fields from primary and related tables". The next form will allow you to limit the output by just these fields and to join in related data (ex: alternate keys/labels). Or download the entire table and cut out the columns after (although this is not recommended for large files - for large files use the next method #2). Most primary tables and all Genbank primary tables have positional information just as you list. 2) Download the complete primary table using ftp/rsync. - http://hgdownload.cse.ucsc.edu/downloads.html - Common name - Choose assembly version - Annotation database - All tables in the Table browser are here in file format as table_name.txt.gz The schema for a table (column definitions) can be found by using the "describe table schema" button next to the "table" pull-down menu. This is good to learn for either method. More FAQ help: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download1 http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html http://genome.ucsc.edu/FAQ/FAQformat.html http://genome.ucsc.edu/FAQ/FAQdownloads.html#download4 http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Please feel free to contact the mailing list support team again if you would like more assistance. Warm regards, Jen UCSC Genome Browser Support On 8/31/10 4:50 PM, Goh, WeeSiong (Sho) wrote: > Hi, > > I need help to download a tab-delimited or csv file containing information > e.g. > Chromosome > Start position > End position > Strand > of GenBank sequences from UCSC genome browser (e.g. DQ539889 to DQ569912). > Please advise. > > Best, > Sho _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
