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

[Ludwig Geistlinger]

Dear Johannes,

Thx for providing the great EnsDb packages!

One question:

As of now, I am able to choose between TxDb and EnsDb for genomic
coordinates of genomic features such as genes, transcripts, and exons.
For the sequences themselves I need the corresponding BSgenome package.

While it is easy to automatically map from a specific TxDb package (eg
TxDb.Hsapiens.UCSC.<hg38>.knownGene) to the corresponding BSgenome package
(here: BSgenome.Hsapiens.UCSC.<hg38>), I wonder how to do that for an
EnsDb package as the package name (eg EnsDb.Hsapiens.v79) contains no
information about the genome build.

A cumbersome option would be to extract the genome_build from the metadata
of the EnsDb package (which would give me for EnsDb.Hsapiens.v79:
'GRCh38') and then ask all existing BSgenome.Hsapiens packages for their
metadata release name (eg 'GRCh38' for BSgenome.Hsapiens.UCSC.hg38).

This however needs all BSgenome.Hsapiens packages installed and takes thus
too much time and space for a programmatic access.

Can you suggest a better way to map from coordinates to sequence (within
the BioC annotation functionality)?

Thanks & Best,
Ludwig





> dear Robert and Ludwig,
>
> the EnsDb packages provide all the gene/transcript etc annotations for all
> genes defined in the Ensembl database (for a given species and Ensembl
> release). Except the column/attribute "entrezid" that is stored in the
> internal database there is however no link to NCBI or UCSC annotations.
> So, basically, if you want to use "pure" Ensembl based annotations: use
> EnsDb, if you want to have the UCSC annotations: use the TxDb packages.
>
> In case you need EnsDbs of other species or Ensembl versions, the
> ensembldb package provides functionality to generate such packages either
> using the Ensembl Perl API or using GTF files provided by Ensembl. If you
> have problems building the packages, just drop me a line and I'll do
> that.
>
> cheers, jo
>
>> On 03 Jun 2015, at 15:56, Robert M. Flight <rflight79 at gmail.com> wrote:
>>
>> 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
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
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