Hello Ajish, We understand that this is inconvenient for certain types of analysis. The original logic was to add more to the track, since there were very few chimp RefSeqs and the human genome was used to help finish the chimp genome.
The group is rethinking this original logic and will use your comments along with others in our decision making processes for future track updates/changes. Your ideas mirror other feedback we have received. On a practical level, human and chimp RefSeqs can be distinguished using the organism assignment. Using the Table browser is an option (as well as the flat files on hgdownload). Link path: refGene.name -> gbCdnaInfo.acc gbCdnaInfo.organism -> organism.id Example output: (you could filter, add more data columns, etc.) #panTro2.refGene.name panTro2.gbCdnaInfo.acc panTro2.gbCdnaInfo.organism panTro2.organism.name NR_027361 NR_027361 299 Homo sapiens NM_001130413 NM_001130413 299 Homo sapiens NM_002978 NM_002978 299 Homo sapiens NM_001009072 NM_001009072 6256 Pan troglodytes NM_030649 NM_030649 299 Homo sapiens NM_153339 NM_153339 299 Homo sapiens NM_017871 NM_017871 299 Homo sapiens NM_001029885 NM_001029885 299 Homo sapiens NM_152228 NM_152228 299 Homo sapiens NM_004421 NM_004421 299 Homo sapiens NM_001012430 NM_001012430 6256 Pan troglodytes NM_032348 NM_032348 299 Homo sapiens Thank you for sharing your comments, we always appreciate user feedback. Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/29/10 9:16 PM, Ajish George wrote: > refFlat from the latest PanTro build contains both chimp and human refseq > mappings. > Why for this genome are the human mappings not separated into the xenoRef > set? > This breaks the RefSeq species specificity since the source species is not > labeled in the table, no? > > -Ajish D. George > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
