dear Ludwig, On 10 Jun 2015, at 10:29, Ludwig Geistlinger <ludwig.geistlin...@bio.ifi.lmu.de<mailto:ludwig.geistlin...@bio.ifi.lmu.de>> wrote:
Dear Johannes, one follow-up question/comment on the EnsDb packages: The reason they escaped my notice (and thus potentially will also others) is that I expected such packages to be named "^TxDb...". What actually argues against sticking to existing Bioc vocabulary and naming eg EnsDb.Hsapiens.v79 TxDb.Hsapiens.Ensembl.hg38.ensGene the reason is that I defined the EnsDb class which is different from the TxDb class (I added some Ensembl specific informations, like gene biotype, that are not covered by the TxDb). I just tried to implement the same functionality as for TxDb classes so that EnsDb can be integrated seamlessly in existing TxDb based workflow, just using the Ensembl annotations. The naming convention for such packages is always: <class name>.<organism>.<version>, thus it was suggested to me to use the naming convention that I'm using at present. For the version I opted to use the Ensembl version instead of the genome version as there are several Ensembl versions for the same genome release and the annotations can change sometimes considerably (or at least did in the past) from Ensembl version to Ensembl version. This naming also allows to have annotation packages from different Ensembl releases installed (or being used in the same R-session) and compare gene models between them etc. (or alternatively, if packages like BSgenome.Hsapiens.NCBI.GRCh38 will indeed make it in the long run: TxDb.Hsapiens.Ensembl.GRCh38.ensGene) This would also have the advantage that genome build and idType could be inferred right from the package name. I agree that that would ease the mapping between BSgenome and EnsDb, but, as explained above, I would like to stick to the Ensembl version instead. I really like the AnnotationHub approach from Martin to get the appropriate DNA sequence for an Ensembl release, so, once I figured out what caused the error in the previous mail, I'll implement a method that returns the correct DNA sequence object for a given EnsDb package. cheers, jo 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 <rfligh...@gmail.com<mailto:rfligh...@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.geistlin...@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.geistlin...@bio.ifi.lmu.de _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
