Entering edit mode
3.1 years ago
ced.gob.cg
▴
10
Hi,
It seems that combining Biomart and Gviz to visualize gene annotation generates strange behavior. For mouse assembly, GRCm39/mm39 is the default now.
In case you have functions written as below - the gene coordinates are returned in reference to mm39 and not mm10 genome assembly. Be careful!
bm <- useMart("ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl")
biomTrack <- BiomartGeneRegionTrack(genome = "mm10",symbol = 'Alb', name = "ENSEMBL", biomart = bm ,transcriptAnnotation = "symbol")
You have to access an archive ensembl version to fix it:
bm <- useMart("ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl",host="http://aug2020.archive.ensembl.org")
Cédric
