Good Morning ib: You can relate these gene names to each other via the knownTo* tables. knownToRefSeq will relate the NM_* and NR_* names to UCSC gene names uc0* and the knownToEnsembl table relates the Ensembl gene names to the UCSC gene names. You can do this join in the table browser, or for example from unix command line tools:
wget -O /dev/stdout \ http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownToEnsembl.txt.gz \ | zcat | sort > knownToEnsembl.txt wget -O /dev/stdout \ http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownToRefSeq.txt.gz \ | zcat | sort > knownToRefSeq.txt join knownToRefSeq.txt knownToEnsembl.txt Resulting in the output: uc001aac.4 NR_024540 ENST00000438504 uc001aae.4 NR_024540 ENST00000438504 uc001aah.4 NR_024540 ENST00000438504 uc001aai.1 NR_024540 ENST00000537342 uc001aak.3 NR_026818 ENST00000417324 uc001aal.1 NM_001005484 ENST00000335137 ... etc ... --Hiram i b wrote: > Hi, > here it is what I need to do: > > I have my cuffdiff outputs with refeence annotation UCSC RefSeq genes > (NM_xxxxx or NR_xxxxx). > Then I have a list of genes which I have pulled out from the UCSC > genome broser (hg19 known gene) and these came out with with gene name > starting with uc00xxxxx > > I need to put them in the same format, e.g. both NM_xxxxx > Then I have another set of genes. These genes have the Ensembl format > e.g ENSG00000131979 > and I need them to be NM_xxxxx format as well > > Thanks! > ib > > On Fri, Jul 27, 2012 at 2:44 AM, Hiram Clawson <[email protected]> wrote: >> Can you please give an example of what your are talking about. >> What is the RefSeq gene format ? >> What is the ensembl format ? >> Where do you find these formats ? >> >> --Hiram >> >> >> On 7/26/12 2:22 PM, i b wrote: >>> Hi, >>> I would like to covert my UCSC RefSeq gene's format into ensembl and vice >>> versa. >>> >>> Does UCSC table browser have any tool? if yes,could you please give me >>> some instructions? >>> >>> Thanks, >>> ib >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
