[Bioc-devel] Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency

Ludwig Geistlinger Ludwig.Geistlinger at bio.ifi.lmu.de
Wed Jun 3 13:03:33 CEST 2015

Dear Bioc annotation team,

Querying TxDb.Hsapiens.UCSC.hg38.knownGene for gene coordinates, e.g. for

BRCA1; ENSG00000012048; entrez:672


> genes(TxDb.Hsapiens.UCSC.hg38.knownGene, vals=list(gene_id="672"))

gives me:

GRanges object with 1 range and 1 metadata column:
      seqnames               ranges strand |     gene_id
         <Rle>            <IRanges>  <Rle> | <character>
  672    chr17 [43044295, 43170403]      - |         672
  seqinfo: 455 sequences (1 circular) from hg38 genome

However, querying Ensembl and NCBI Gene

the gene is located at (note the difference in the end position)

Chromosome 17: 43,044,295-43,125,483 reverse strand

How is the inconsistency explained and how to extract an ENSEMBL/NCBI
conform annotation from the TxDb object?
(I am aware of biomaRt, but I want to explicitely use the Bioc annotation


Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München

Tel.: 089-2180-4067
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de

More information about the Bioc-devel mailing list