Hello Swapnil, To explain some background, in the last few years the track named "Known Genes" has been replaced with a new track called "UCSC Genes". The overall idea is the same (cluster known transcripts into genes), but the processing is different, which produces different files. For a certain time during the transition, both versions of the track were available. Starting in hg19, as you have noticed, only the UCSC Genes track is now available.
Links to NCBI accessions (when available) and other identifiers are still contain in the dataset, only in different locations: knownGene (default table for track "UCSC Genes") kgAlias = primary set of alternate identifiers kgXref = expanded set of alternate identifiers Using the Table browser is probably the best way to view the schema relationships between the data, join tables as desired, and create output in the format you prefer. Start with the UCSC Genes track and with the default table selected (knownGene) use the "describe table schema" button to view data relationships. Then, to output data from more than one table, use output format "selected fields from both primary and related tables". From here you can select fields from the associated tables (add in NCBI accessions or other identifiers) and output a custom file to recreate what the file KnownGeneOld2.txt used to be. Table browser help: http://genome.ucsc.edu/cgi-bin/hgTables http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#SelectedFields Hopefully this helps to get you started. Please let us know if you have questions with the query or data, Jen --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/29/10 4:52 AM, Swapnil Potdar wrote: > Hi, > > We used to have a file KnownGeneOld2.txt till Hg18 release. > > I was looking for the same file for the same file for Hg19. > > Basically KnownGene.txt file used to have the NCBI accessions which were > replaced by the UCSC accession numbers. > > Could you please throw some light on how that file can be generated or how to > convert these UCSC Ids in to NCBI accessions? > > > Regards, > > Swapnil Potdar > > DISCLAIMER > ========== > This e-mail may contain privileged and confidential information which is the > property of Persistent Systems Ltd. It is intended only for the use of the > individual or entity to which it is addressed. If you are not the intended > recipient, you are not authorized to read, retain, copy, print, distribute or > use this message. If you have received this communication in error, please > notify the sender and delete all copies of this message. Persistent Systems > Ltd. does not accept any liability for virus infected mails. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
