Chromosme Name: "CHR_HSCHR19..."
0
0
Entering edit mode
rbenel ▴ 40
@rbenel-13642
Last seen 19 months ago
Israel

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" 

ENSG00000282214

CHR_HSCHR16_CTG2

531239

531551

tslNA

CAPN15

processed_transcript

havana

 

biomart ensembl grch38 • 838 views
ADD COMMENT
0
Entering edit mode

Why do you think anything needs to be corrected?

ADD REPLY
0
Entering edit mode

I understand it is a patch, so if we parse "CHR_HSCHR16_CTG2" we can understand it is from Chr 16? 

ADD REPLY

Login before adding your answer.

Traffic: 697 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6