Sorry Malcolm, there isn't a generic method for all genomes at UCSC. This is a most interesting example you have here. Usually chrM at Ensembl is: "Mt"
Newer genome assemblies at UCSC are including two tables: ensemblLift ucscToEnsembl Which allow translation of UCSC names to Ensembl names and coordinate conversions for haplotypes and other random bits that might be located in a different coordinate system. For example: $ hgsql -e "select * from ensemblLift;" hg19 +-----------------+----------+ | chrom | offset | +-----------------+----------+ | HSCHR4_1 | 69170076 | | HSCHR17_1 | 43384863 | | HSCHR6_MHC_APD | 28696603 | | HSCHR6_MHC_COX | 28477796 | | HSCHR6_MHC_DBB | 28696603 | | HSCHR6_MHC_MANN | 28696603 | | HSCHR6_MHC_MCF | 28696603 | | HSCHR6_MHC_QBL | 28696603 | | HSCHR6_MHC_SSTO | 28659142 | +-----------------+----------+ $ hgsql -e "select * from ucscToEnsembl;" hg19 | grep MHC chr6_ssto_hap7 HSCHR6_MHC_SSTO chr6_qbl_hap6 HSCHR6_MHC_QBL chr6_mcf_hap5 HSCHR6_MHC_MCF chr6_mann_hap4 HSCHR6_MHC_MANN chr6_cox_hap2 HSCHR6_MHC_COX chr6_dbb_hap3 HSCHR6_MHC_DBB chr6_apd_hap1 HSCHR6_MHC_APD It would be a useful process to go back over some of the older popular genomes to add these conversion tables. --Hiram Cook, Malcolm wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
