Hi Andrew, You can get the information for KnownGene using the table browser: Select your assembly (hg19), the group (Genes and Gene Prediction Tracks), the track (UCSC genes), the table (knownGene), and change output format to "sequence". Region should be left as genome unless you want a more specific region. Click on " get output"(it should default to "genomic") and hit "submit". On the following page, you will be able to choose which regions you want to output. Upstream is not on by default, so click the button next to it and change the number of bases to your liking. I recommend looking over the other options and changing them to your liking.
You can also access the knownGeneMrna table from the table browser by selecting it under table in the main page. However, it cannot display the upstream regions, since that table only contains the MRNA sequences themselves. You can also get these tables from our downloads page here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ This is the raw data however, so the table browser would be better suited to give you what you need. I hope this answers your question. Please contact us again if you have further inquiries Antonio Coelho UCSC Genome Bioinformatics Group Andrew Yee wrote: > Hi, I would like to download the knownGeneMrna table. As part of the > download, I would like to automatically include 100 bp of genomic sequence > upstream. I've encountered a file where this has automatically been > generated for Hg18, and I would like to do the same for the Hg19 build. Is > there a way to do this with the table browser? How about with the ftp site? > > Thanks, > Andrew > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
