Hi Andrew, The experiment list is in the encodeExp table in the hgFixed database. (If you are using the Table Browser to get to it, you can see the hgFixed database by changing the "group" to "All Tables.")
The cell type data is not in a table, but it is available in the cv.ra file from our ftp server, here: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/encode/cv.ra There is a handy tool in the Genome Browser source tree, raToTab, that will convert the cv.ra file into a tabular format for loading into a database. The source tree is available from: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads Run raToTab without any arguments to see its usage statement: $ raToTab raToTab - Convert ra file to table. usage: raToTab in.ra out.tab options: -cols=a,b,c - List columns in order to output in table Only these columns will be output. If you Don't give this option, all columns are output in alphabetical order -head - Put column names in header If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 7/20/12 2:26 AM, Andrew Jefferson wrote: > Hello, > > I am using the wonderful resources that you have but I am stuck on one > thing, I am sorry if I am missing something but I haven't ben able to find > an answer online so I'm dropping you an email. > > Is the data on ENCODE cell types ( > http://genome.ucsc.edu/ENCODE/cellTypes.html) available in the MySql > database somewhere? I would like to be able to join the cell information to > the genetic data. > > Similarly is the ENCODE experiment list ( > http://genome.ucsc.edu/ENCODE/dataSummary.html) contained in a table/tables > in the main database? > > Thanks, > Andrew Jefferson > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
