Hi,

I have requested a biotype from biomart in the "attributes" section, and some of the results are returned with this style chromosome name "CHR_HSCHR19_2_CTG2". How can I correct this? 

library(biomaRt)

#get annotations for processed transcripts 
mart  <- biomaRt::useMart( biomart = "ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", dataset = "hsapiens_gene_ensembl")

biotypes = c("processed_transcript")
sources = c("havana", "ensembl_havana")
status = c("KNOWN", "NOVEL")

my_filters =c("biotype")
my_values = list(TRUE, biotypes, sources)

my_attributes = c("ensembl_gene_id","chromosome_name","start_position", 
                  "end_position", "transcript_tsl","external_gene_name", "gene_biotype")

my_annotations = getBM(attributes = my_attributes, 
                               filters = my_filters, 
                               values = my_values, 
                               mart = mart, 
                               uniqueRows = TRUE, #deletes duplicate rows 
                               bmHeader=FALSE) #default 

EX. 

"ensembl_gene_id" "chromosome_name" "start_position"  "end_position" "transcript_tsl" "external_gene_name" "gene_biotype"  "source"