How to get Cytogenetic band for muscles gene by using Biomart or other tools in R
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@c209ec01
Last seen 9 days ago
United States

I'm trying to find out Cytogenetic band for mouse gene by using attributes=c("band"), but the outcome is so weird that all "band" column show "q". \ How can I fix this?\ When I search on NCBI, they give some positions such as "qE13".\ How can I actually obtain this band position information using Biomart?

## read file
M_Pan <- read_excel("Murine.xlsx")
## Get mart
M_mart <-  useMart(biomart = "ensembl", dataset = "mmusculus_gene_ensembl",host = "www.ensembl.org")
## annotation
Mattributes <- getBM(attributes = c("mgi_symbol","ensembl_gene_id","entrezgene_id", 'chromosome_name', 'band'),
                     filters = "mgi_symbol", values = unique(M_Pan$Genename),
                     mart = M_mart)

head(M_attributes,3)

## The result is below, how can I fix the "band" column?

#  mgi_symbol    ensembl_gene_id.    entrezgene_id chromosome_name band start_position end_position
#1      Scmh1 ENSMUSG00000000085         29871               4                     q      120262478    120387383
#2      Ccnd2 ENSMUSG00000000184         12444               6                      q      127102125    127129156
#3     Btbd17 ENSMUSG00000000202         72014              11                     q      114682043    114686771
Annotation biomaRt ensembldb • 63 views
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