Hi All,

Sorry for the naive question! I was trying to retrieve some coordinates (start and end positions) from biomaRt and I'm not sure if I'm doing things right…

Problem definition: For a gene, retrieve the 5'UTR and exon coordinates for the most common isoform of the gene.

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library(biomaRt)
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")

getAtt <- c('chromosome_name', 'start_position', 'end_position', 'strand','exon_chrom_start','exon_chrom_end',
        '5_utr_start','5_utr_end','3_utr_start','3_utr_end')

elocs <- getBM(attributes=getAtt,filters="hgnc_symbol",value="ZMYM4",mart=ensembl)
print(elocs)

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However, this would give me the coordinates for all isoforms and it would be difficult to get the coordinates for the most common isoform. How can I identify the most common isoform?

many thanks!

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