Hi,

I have a getBM query for which I want to retrieve all unique mouse genes. However I receive "duplicate" entries, as I will receive an entry for each start/end site that exists in the DB.

These are unique entries as the start/end site differ, but they have the same gene id/external gene name/mgi symbol etc...

Is there a way to get the "gene summary" per gene? In other words the max location on the chromosome?

MouseAnnotations <- getBM(attributes = c("ensembl_gene_id", "mgi_symbol", "ensembl_transcript_id",
                                               "chromosome_name", "external_gene_name",
                                               "gene_biotype", "strand", "transcript_start", "transcript_end"),
                                mart = mouse, 
                          uniqueRows = T)

Thanks!

I'm not able to test this comprehensively today, but I think you're seeing this behaviour because you're asking for transcript level information, so you get start and end points for all transcripts of each gene.

Maybe try only asking for gene related attributes e.g. something like:

MouseAnnotations2 <- getBM(attributes = c("ensembl_gene_id", "mgi_symbol",
                                         "chromosome_name", "external_gene_name",
                                         "gene_biotype", "strand", "start_position", "end_position"),
                          mart = mouse, 
                          uniqueRows = T)