update: this approach bases on Martin's suggestion and I think is ideal for
EnsDb or any Ensembl based annotation packages. It's not required to install an
explicit genome package, but load (and eventually cache) dynamically the
correct genomic sequence from Ensembl via AnnotationHub. That way chromosome
names, variants etc are perfectly aligned. Also, this guarantees that the
genome version and gene definitions, both from Ensembl match.
Example code (is now also included in the ensembldb vignette):
library(AnnotationHub)
library(EnsDb.Hsapiens.v75)
library(Rsamtools)
ah <- AnnotationHub()
edb <- EnsDb.Hsapiens.v75
## get the Ensembl version
eVersion <- metadata(edb)[metadata(edb)$name=="ensembl_version", "value"]
## query all available files for the Ensembl version
eData <- query(ah, c(organism(edb), paste0("release-", eVersion)))
eData
## retrieve the *dna.toplevel.fa file; this might take some time.
Dna <- ah[["AH20439"]]
## generate an index if none is available
if(is.na(index(Dna))){
indexFa(Dna)
Dna <- FaFile(path(Dna))
}
## get start/end coordinates of all genes
genes <- genes(edb)
## subset to all genes that are encoded on chromosomes for which
## we do have DNA sequence available.
genes <- genes[seqnames(genes) %in% seqnames(seqinfo(Dna))]
## get the gene sequences, i.e. the sequence including the sequence of
## all of the gene's exons and introns
geneSeqs <- getSeq(Dna, genes)
cheers, jo
On 09 Jun 2015, at 11:38, Rainer Johannes
<johannes.rai...@eurac.edu<mailto:johannes.rai...@eurac.edu>> wrote:
dear Ludwig,
On 09 Jun 2015, at 10:46, Ludwig Geistlinger
<ludwig.geistlin...@bio.ifi.lmu.de<mailto:ludwig.geistlin...@bio.ifi.lmu.de>>
wrote:
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)?
agree, there's no easy mapping (yet). I'll implement a method
"suggestGenomePackage" in the ensembldb package. In the long run I hope that
also NCBI BSgenome packages (like the BSgenome.Hsapiens.NCBI.GRCh38) will
become available for all species... that would make the mapping much easier...
cheers, jo
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
<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<mailto: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<mailto:ludwig.geistlin...@bio.ifi.lmu.de>
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