Hello, The track sno/miRNA in the Gene and Gene predictions track group has this type of information. Go into the browser and click on the track name to read about the contents, methods, etc. Then click on the "view table schema" link to see the primary table "wgRna". The table/file is in BED format. You can download data from the Table browser or ftp the table from the Downloads server. The table name is the same as the file name, except the file ends with a .txt.gz and an associated table schema ends in .sql
To merge with RefSeqs, use the Table browser to send the contents of the primary RefSeq Genes (refGene, genePred format) table and the primary sno/miRna table to Galaxy and do a full join there. Or, create your own tools to do the merge based on coordinates using your own tools. Descriptions of file formats: http://genome.ucsc.edu/FAQ/FAQformat Download options: http://genome.ucsc.edu/FAQ/FAQdownloads#download1 Database tables are in the directory Downloads -> common name -> release -> annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ or ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/<table name> Coordinate help: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms We hope this helps. Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "chunjiang he" <[email protected]> wrote: > From: "chunjiang he" <[email protected]> > To: [email protected] > Sent: Friday, December 4, 2009 1:54:11 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] about miRNA target sites > > Hi all, > I am looking for the miRNA target sites files to download. I prefer > the > coordinate on chromosome. like: > > RefSeq Name microRNA Position Seed dGduplex dGopen ddG Conservation > Chromosome Start End Strand Name > NM_000014 A2M hsa-miR-106a 102 6:0:0 -10.6 -11.02 0.42 0.013 12 > 9111585 > 9111590 - A2M|hsa-miR-106a|1 > > This is provided by PITA database. But I don't know if UCSC and other > databases contain this information. Thanks. > > Best, > Chunjiang > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
