Hello Mali, To see which version of Ensembl we are using you can click on any of the items in the Ensembl track. This will take you to a details page for that item which should include the Ensembl version number in the title of the details page. Currently we are using version 50.
You will need to get the information one of two ways. You can go to the table browser (http://genome.ucsc.edu/cgi-bin/hgTables) and select: group: Genes and Gene Prediction Tracks track: Ensembl Genes table: ensGene region: genome output format: BED - browser extensible data You might also want to receive the file as a gzip compressed file. Alternatively, you can get the same file here: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ensGene.txt.gz Once you have this file, from the command line type: zcat ensGene.txt.gz | awk '{print $3,$5,$6,$2}' This will give you a BED file with txStart,txEnd coordinates. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [EMAIL PROTECTED] Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu mali salmon wrote: > Dear Sir/Madam > I would like to have a list of all ensembl transcripts in UCSC BED format, > and I thought of downloading it from your table browser. > Can you please tell me on which Ensembl version your Ensembl genes track is > based on? > I can see that this track was last updated at 2008-08-08 which is fit to > Ensembl50, can you confirm that? > In addition, does this track contains all the ensembl transcripts of the > specific Ensembl version? > Looking forward to your reply > Thanks > Mali > > > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
