Hello, Using the UCSC Table browser, select the clade/genome/assembly/group and choose UCSC Genes. Set the table to knownGene (for complete alignment data) or just kgAlias (for two column output) or join both together in the output. Upload the list of IDs and output the results or save as a custom track to view in the browser, save in a session, or more file manipulations within the Table browser.
The search is recursive when using the kgAlias table, meaning that if one of your gene names matches a UCSC Gene, all other known aliases will also be in the output. This can sometimes produce too much duplicated/unwanted output. Another option is to ftp the file from our Downloads server and do a unix join between your list and table. http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ ftp file kgAlias.txt.gz (and knownGene.txt.gz). Schema for kgAlias Database: hg18 Primary Table: kgAlias Row Count: 458,806 Format description: Link together a Known Gene ID and a gene alias field example SQL type info description kgID uc001aaa.2 varchar(40) values Known Gene ID alias BC032353 varchar(80) values a gene alias We hope this is helpful, Jennifer Jackson UCSC Genome Bioinformatics Group Adjailia Malik wrote: > Hi, > > i have a list of gene names (more than 40.000), like Nr2f6,Zswim6, etc... and > i want to convert it to UCSC geneID like uc002nfq.1m, uc003jsr.1, etc ... > > Wich table of the database should i use ? > thanks. > > Malik > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
