Hiram, Is there a similar approach for chromosomal identifiers? (i.e. chrM in dm3 is dmel_mitochondrion_genome at ensemble)
Or better, an SQL query for same? Thx Malcolm Cook Stowers Institute for Medical Research - Bioinformatics Kansas City, Missouri USA > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Hiram Clawson > Sent: Thursday, March 31, 2011 4:18 PM > To: Rajasimha, Harsha (NIH/NEI) [C] > Cc: '[email protected]' > Subject: Re: [Genome] How to generate mapping between Ensembl > and refseq transcript IDs > > Good Afternoon Dr. Rajasimha: > > Start with the mm9.knownGene table. Use the knownToEnsembl > table to link names to Ensembl > names, and the mm9.kgXref.refseq table to get the RefSeq > name. Your multiple table > join selection will display: > > #mm9.knownGene.name mm9.knownToEnsembl.value > mm9.ensGene.name mm9.ensGtp.gene mm9.ensGtp.transcript > mm9.ensGtp.protein > mm9.ensPep.name mm9.kgXref.refseq > c007npi.1 ENSMUST00000001538 ENSMUST00000001538 > ENSMUSG00000001497 ENSMUST00000001538 > ENSMUSP00000001538 ENSMUST00000001538 NM_011041 > > --Hiram > > Rajasimha, Harsha (NIH/NEI) [C] wrote: > > I need a mapping between Ensembl transcript ID and Refseq > transcript ID (from refflat.txt file). > > I am trying to use the UCSC table browser to generate such > a tab delimited output - however, I am unable to do so. > > I get N/A for refseq transcript ID column values. > > > > #mm9.ensGtp.gene mm9.ensGtp.transcript > mm9.ensGene.name mm9.ensGene.chrom > mm9.refFlat.geneName mm9.refFlat.name > > ENSMUSG00000090025 ENSMUST00000160944 > ENSMUST00000160944 chr1 n/a n/a > > ENSMUSG00000064842 ENSMUST00000082908 > ENSMUST00000082908 chr1 n/a n/a > > ENSMUSG00000051951 ENSMUST00000162897 > ENSMUST00000162897 chr1 n/a n/a > > ENSMUSG00000051951 ENSMUST00000159265 > ENSMUST00000159265 chr1 n/a n/a > > ENSMUSG00000051951 ENSMUST00000070533 > ENSMUST00000070533 chr1 n/a n/a > > > > Please help in generating this mapping as I need to > integrate transcript IDs from Ensembl with refseq. > > > > Thank you! > > > > HARSHA K RAJASIMHA, Ph.D. > > Digicon Contractor, ITMB/NNRL/NEI > > Bioinformatics Programmer / Analyst > > National Institutes of Health > > 6 CENTER DR RM 303 MSC 0610 > > BETHESDA MD 20892-0610 > > Tel: 301-402-5734 > > Fax: 301-480-1769 > > Email: [email protected] > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
