Hello Sanjit, These data are custom tracks, so are not available on the UCSC public mySQL server. The data authors may have a mySQL database for public access, but you will need to contact them to find out.
To obtain the data using UCSC's tools, you will need to use the link from the source to load the custom tracks, then use the Table browser to download the source files. Using the link in your email, go to that web site and scroll to the bottom of the page to find: External Links Links to Custom tracks on the UCSC Genome Browser (<-click on this) When I did this, it opened a UCSC Browser window in the Human Mar. 2006 (NCBI36/hg18) assembly with the custom tracks from the source loaded and open. To download data, next use the top navigation bar to go to "Tables". The result page is the Table browser form. Help: http://genome.cse.ucsc.edu/goldenPath/help/hgTablesHelp.html Basic query to download custom track data: 1) set clade/genome/assembly to hg18 2) set group to "Custom Tracks" (top of pull down menu) 3) the tracks listed as those you have loaded in your session as a custom track. It will be the set from the linked site plus any custom tracks you already had loaded, if any. Choose the track of interest. Only one can be selected at a time. 4) leave remaining options as default (including table, unless there is more than one and you are trying to download each. Again, this must be done one at a time.) 5) name file and click on "get output". The file representing the data in the primary table should download. To understand the file contents, click on "describe table schema" next to the option "table" in the form. To associate track contents with table names, use the Genome browser and click on the custom track names to read the descriptions provided by the authors. You might try contacting the authors to see what they have available as files for ftp or other supporting documentation. They would also be the best source if you have question about content. Please let us know if you have any other questions, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ --- original email --- Subject: A quection regarding MySQl database From: Sanjit Pandey <[email protected]> Date: Tue, 6 Apr 2010 19:42:02 -0500 To: [email protected] Hi, I am trying to locate the database for "Follicular Lymphoma Tumour BAC Fingerprint Database" (http://flt.bcgsc.ca/). But I am not able to identify the database for these data. I connected to the mySQL database using mysql --user=genome --host=genome-mysql.cse.ucsc.edu I can see a list of databases but don't know which database has what information. Is there a help file that has these information? Thanks Sanjit _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
