update: seems something is strange with the index... when I load the ensembl-77 DNA for mouse I get two files, the fasta file and the index and I can extract the sequences, while in the example below I just got the fasta file
On 10 Jun 2015, at 10:11, Rainer Johannes <johannes.rai...@eurac.edu<mailto:johannes.rai...@eurac.edu>> wrote: Dear Martin, the AnnotationHub approach looks awesome! However, somehow it does not work for me, I always get an error: library(AnnotationHub) library(Rsamtools) library(GenomicFeatures) ah <- AnnotationHub() ## somehow I don't see DNA sequences for release-80... thus using 75 query(ah, c("Takifugu", "release-75")) ## load the gtf and the dna.toplevel.fa gtf <- ah[["AH10717"]] dna <- ah[["AH20637"]] ## create txdb and get exons: txdb <- makeTxDbFromGRanges(gtf) exons <- exons(txdb) ## getting the sequences getSeq(dna, exons) and I get the following error: Error in value[[3L]](cond) : 'open' index failed file: /Users/jo/~/.AnnotationHub/24732 In addition: Warning message: In doTryCatch(return(expr), name, parentenv, handler) : [fai_load] fail to open FASTA index. ## creating the index indexFa(dna) ## trying again: getSeq(dna, exons) Error in value[[3L]](cond) : record 1 (MT:1-68) was truncated file: /Users/jo/~/.AnnotationHub/24732 This one is from the current R-devel, but I get the same error with the stable version... any idea? cheers, jo my session info: > sessionInfo() R Under development (unstable) (2015-06-06 r68485) Platform: x86_64-apple-darwin14.4.0/x86_64 (64-bit) Running under: OS X 10.10.4 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicFeatures_1.20.1 AnnotationDbi_1.30.1 Biobase_2.28.0 [4] Rsamtools_1.20.4 Biostrings_2.36.1 XVector_0.8.0 [7] GenomicRanges_1.20.4 GenomeInfoDb_1.4.0 IRanges_2.2.3 [10] S4Vectors_0.6.0 BiocGenerics_0.14.0 AnnotationHub_2.0.2 loaded via a namespace (and not attached): [1] Rcpp_0.11.6 magrittr_1.5 [3] GenomicAlignments_1.4.1 zlibbioc_1.14.0 [5] BiocParallel_1.2.2 xtable_1.7-4 [7] R6_2.0.1 stringr_1.0.0 [9] httr_0.6.1 tools_3.3.0 [11] DBI_0.3.1 lambda.r_1.1.7 [13] futile.logger_1.4.1 htmltools_0.2.6 [15] digest_0.6.8 interactiveDisplayBase_1.6.0 [17] shiny_0.12.0 rtracklayer_1.28.4 [19] futile.options_1.0.0 bitops_1.0-6 [21] biomaRt_2.24.0 RCurl_1.95-4.6 [23] RSQLite_1.0.0 mime_0.3 [25] stringi_0.4-1 BiocInstaller_1.18.2 [27] XML_3.98-1.2 httpuv_1.3.2 On 09 Jun 2015, at 16:25, Martin Morgan <mtmor...@fredhutch.org<mailto:mtmor...@fredhutch.org>> wrote: On 06/08/2015 11:43 PM, Rainer Johannes wrote: 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. Two other sources of Ensembl TxDb's are GenomicFeatures::makeTxDbFromBiomart() and AnnotationHub. For the latter, I'll add a variant of the following to the AnnotationHub HOWTO vignette http://bioconductor.org/packages/devel/bioc/html/AnnotationHub.html later today. ## Gene models _Bioconductor_ represents gene models using 'transcript' databases. These are available via packages such as [TxDb.Hsapiens.UCSC.hg38.knownGene](http://bioconductor.org/packages/TxDb.Hsapiens.UCSC.knownGene.html), or can be constructed using functions such as `[GenomicFeatures](http://bioconductor.org/packages/GenomicFeatures.html)::makeTxDbFromBiomart()` or `GenomicFeatures::makeTxDbFromGRanges()`. _AnnotationHub_ provides an easy way to work with gene models published by Ensembl. Here we discover the Ensemble release 80 r esources for pufferfish,_Takifugu rubripes_ ```{r takifugu-gene-models} query(ah, c("Takifugu", "release-80")) ``` We see that there is a GTF file, as well as various DNA sequences. Let's retrieve the GTF and top-level sequence files. The GTF file is imported as a _GRanges_ instance, the DNA sequence as a compressed, indexed Fasta file ```{r takifugi-data} gtf <- ah[["AH47101"]] dna <- ah[["AH47477"]] head(gtf, 3) dna head(seqlevels(dna)) ``` It is trivial to make a TxDb instance ```{r takifugi-txdb} library(GenomicFeatures) txdb <- makeTxDbFromGRanges(gtf) ```` and to use that in conjunction with the DNA sequence, e.g., to find exon sequences of all annotated genes. ```{r takifugi-exons} library(Rsamtools) # for getSeq,FaFile-method exons <- exons(txdb) getSeq(dna, exons) ``` Some difficulties arise when working with this partly assembled genome that require more advanced GenomicRanges skills, see the [GenomicRanges](http://bioconductor.org/packages/GenomicRanges.html) vignettes, especially "GenomicRanges HOWTOs" and "An Introduction to GenomicRanges". 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> _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. 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