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

[Robert M. Flight]

Ludwig,

If you do this search on the UCSC genome browser (which this annotation
package is built from), you will see that the longest variant is what is
shown

http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=Human&db=hg38&position=brca1&hgt.positionInput=brca1&hgt.suggestTrack=knownGene&Submit=submit&hgsid=429339723_8sd4QD2jSAnAsa6cVCevtoOy4GAz&pix=1885

If instead of "genes" you do "transcripts", you will see 20 different
transcripts for this gene, including the one listed by NCBI.

I havent tried it yet (haven't upgraded R or bioconductor to latest
version), but there is now an Ensembl based annotation package as well,
that may work better??
http://bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v79.html

-Robert



On Wed, Jun 3, 2015 at 7:04 AM Ludwig Geistlinger <
Ludwig.Geistlinger at bio.ifi.lmu.de> wrote:

> Dear Bioc annotation team,
>
> Querying TxDb.Hsapiens.UCSC.hg38.knownGene for gene coordinates, e.g. for
>
> BRCA1; ENSG00000012048; entrez:672
>
> via
>
> > 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
> http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000012048
> http://www.ncbi.nlm.nih.gov/gene/672
>
> 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
> functionality).
>
> Thanks!
> Ludwig
>
>
> --
> 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
>
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