Gene Locus to ENSEMBL ID
Is there some way (biomaRt or not) that will allow me to convert the gene locus (NM_###) to it's ensembl gene id?
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Biostar
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Scott McKay •
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Scott McKay •
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If you want to convert RefSeq 'NM' or 'NR' identifiers, then use refseq_mrna or refseq_ncrna attributes, repectively, as I mention at the end of my answer, here: A: Affymetrix Human Genome U133 Plus 2.0 Array
Also a practical example shown here by another user: A: biomaRt doesn't convert refseq_rna to flybase_gene_id
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Kevin Blighe
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What have you tried? Did you look at
listAttributes()etc in biomaRt? Search for other packages such asorg.Hs.eg.db?I looked at
searchAttributes(mart=ensembl, pattern=locus)and then searched the Attributes for some loci information but turned up nothingAssuming this is about RefSeq accession numbers, note that NM prefixes are used for curated protein-coding transcripts, not genomic loci. Associating an accession number with the wrong entity type may mislead you.