using biomaRt to query cds coordinates with respect to the transcript for a given gene
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Andrew Yee ▴ 350
@andrew-yee-2667
Last seen 7.3 years ago
I'm in interested in the start and stop locations for the coding DNA sequence. For example, for the reference squence for AKT1, NM_001014431, the cds location in NCBI is reported as 341..1783 (see also http://www.ncbi.nlm.nih.gov/nuccore/62241012). I'm now working using biomaRt and using the Ensembl accession number ENST00000349310 as follows: library('biomaRt') ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") getBM(attributes=c('cds_start'), filters='ensembl_transcript_id', values='ENST00000349310', mart=ensembl) getBM(attributes=c('transcript_start'), filters='ensembl_transcript_id', values='ENST00000349310', mart=ensembl) However, these give me results with respect to the genomic coordinates. Is there a way to give the start of the cds with respect to the transcript? Thanks, Andrew [[alternative HTML version deleted]]
biomaRt biomaRt • 1.3k views
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