Ensembl id missing when retrieving through biomart

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3.5 years ago

iibrams07 ▴ 10

I have a set of apparently hgnc_symbol assigned genes that I retrieved with biomart. It turns our that many of the corresponding ensembl id are missing i.e. replaced with NaN. How it can be that there are no ensembl id for so many genes? Is there a way to find them?

I used the following command in retrieving the data:

results <- getBM(attributes=c("ensembl_gene_id","hgnc_symbol","transcript_biotype"),filters = c("transcript_biotype"), values=list("protein_coding"), mart=ensembl)

Thanks

biomart • 797 views

ADD COMMENT • link updated 3.5 years ago by Ram 45k • written 3.5 years ago by iibrams07 ▴ 10

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Different organisations have different rules about what is annotated or not. I am assuming that these genes in question have low evidence of even existing, or relate to obscure non-coding transcripts that may not yet have been reviewed by HGNC. Can you please paste some example IDs?

ADD REPLY • link 3.5 years ago by Kevin Blighe 89k

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