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
