Getting chromosome of unusual chromosome names e.g. 'CHR_HSCHR8_8_CTG1'
I made a biomaRt query:
library(biomaRt)
mart = useMart('ensembl', dataset = 'hsapiens_gene_ensembl')
genes = getBM(attributes = c("chromosome_name","start_position", "hgnc_symbol", "uniprot_gn_symbol", "uniprot_gn_id"), mart = mart, values = list("protein_coding",c(1:22)))
Most of the chromosome_name values are regular numbers 1 to 22. However, some are unusual, such as CHR_HSCHR14_7_CTG1.
Some don't have obvious chromosome identifiers e.g. CHR_HG2334_PATCH
How can I find the 'regular' chromosome name of names like these?
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Someone may know more of the specifics, but it's probably some alternative contig for a region on chromosome 14. The human reference genome will have a bunch of alternative and unplaced contigs along with the main chromosomes and MT genome.