Hello Pedro, The Table Browser tool is a great tool for this type of query. Locate the tool in the browser by pressing 'Tables' from the top blue navigation bar.
Help page: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Follow this general path for your query: 1) Create a custom track that contains only the refSeq sequences of interest using your list of identifiers (they can be pasted in or uploaded). Send results back to the table browser. Main RefSeq table: group: Gene and Gene Prediction Tracks track: RefSeq Genes table: refGene. Help section: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#FilterSingle 2) Intersect the est data with this custom track. There are several options that allow the user to specify overlap conditions. Main EST table: group: mRNA and EST tracks track: Human ESTs table: est Help section: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection 3. Retrieve the data as desired (a downloaded file, a custom track to view in the target assembly browser, a custom track to send back to Table browser for new queries, etc). Help section: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#OutputFormats 4. To obtain additional information about the est data not contained in the initial output, additional intersection cycles may be required, using the est identifiers as a custom track or as pasted in lists. Use the "describe table schema" to view individual table contents, linked tables (and contents), and sample data. Help section: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#SelectedFields Please let us know if you need more help with specifics as you work through the query, Jennifer Jackson UCSC Genome Bioinformatics Group _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
