Hi Julie, Julie Zhu wrote: > Hi Herve, > > I tried to install the Zebrafish genome but without success. Could you > please let me know why? Thanks! > > Best regards, > > Julie > >> source("http://bioconductor.org/biocLite.R") >> biocLite("BSgenome.Drerio.UCSC.danRer5") > Running biocinstall version 2.4.11 with R version 2.9.0 > Your version of R requires version 2.4 of Bioconductor. > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ?BSgenome.Drerio.UCSC.danRer5? is not available This is because binary versions of the package are not available yet. If your system is configured to install from source, you can try to use biocLite() with 'type="source"'. Cheers, H. >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-apple-darwin8.11.1 > > locale: > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ChIPpeakAnno_1.0.0 GenomicFeatures_0.0.1 BSgenome_1.12.3 > Biostrings_2.12.3 IRanges_1.2.1 multtest_2.0.0 > [7] Biobase_2.4.1 biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] MASS_7.2-46 RCurl_0.94-1 splines_2.9.0 survival_2.35-4 > tools_2.9.0 XML_2.5-3 > > > On 7/29/09 12:41 AM, "hpages at fhcrc.org" <hpages at="" fhcrc.org=""> wrote: > >> Hi Julie, >> >> The Zebrafish (Danio rerio) genome is now available in BioC release >> and will soon be in BioC devel: >> >>> library(BSgenome) >>> available.genomes() >> [1] "BSgenome.Amellifera.BeeBase.assembly4" >> [2] "BSgenome.Amellifera.UCSC.apiMel2" >> [3] "BSgenome.Athaliana.TAIR.01222004" >> [4] "BSgenome.Athaliana.TAIR.04232008" >> [5] "BSgenome.Btaurus.UCSC.bosTau3" >> [6] "BSgenome.Btaurus.UCSC.bosTau4" >> [7] "BSgenome.Celegans.UCSC.ce2" >> [8] "BSgenome.Cfamiliaris.UCSC.canFam2" >> [9] "BSgenome.Dmelanogaster.UCSC.dm2" >> [10] "BSgenome.Dmelanogaster.UCSC.dm3" >> [11] "BSgenome.Drerio.UCSC.danRer5" >> [12] "BSgenome.Ecoli.NCBI.20080805" >> [13] "BSgenome.Ggallus.UCSC.galGal3" >> [14] "BSgenome.Hsapiens.UCSC.hg17" >> [15] "BSgenome.Hsapiens.UCSC.hg18" >> [16] "BSgenome.Hsapiens.UCSC.hg19" >> [17] "BSgenome.Mmusculus.UCSC.mm8" >> [18] "BSgenome.Mmusculus.UCSC.mm9" >> [19] "BSgenome.Ptroglodytes.UCSC.panTro2" >> [20] "BSgenome.Rnorvegicus.UCSC.rn4" >> [21] "BSgenome.Scerevisiae.UCSC.sacCer1" >> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("BSgenome.Drerio.UCSC.danRer5") >> ... >>> library(BSgenome.Drerio.UCSC.danRer5) >>> Drerio >> Zebrafish genome >> | >> | organism: Danio rerio (Zebrafish) >> | provider: UCSC >> | provider version: danRer5 >> | release date: Jul. 2007 >> | release name: Sanger Institute Zv7 >> | >> | single sequences (see '?seqnames'): >> | chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 >> chr10 chr11 >> | chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 >> chr21 chr22 >> | chr23 chr24 chr25 chrM >> | >> | multiple sequences (see '?mseqnames'): >> | Zv7_NA Zv7_scaffold upstream1000 upstream2000 upstream5000 >> | >> | (use the '$' or '[[' operator to access a given sequence) >> >>> Drerio$chr1 >> 56204684-letter "MaskedDNAString" instance (# for masking) >> seq: >> CACACACTCATACACTACGGCCAGTGTAGTTGATCA...GGAGGATCTGACGTCTGTGAGCAAACAC AAACACAC >> masks: >> maskedwidth maskedratio active names desc >> 1 150400 2.675934e-03 TRUE AGAPS assembly gaps >> 2 288 5.124128e-06 TRUE AMB intra-contig ambiguities >> 3 26544901 4.722898e-01 FALSE RM RepeatMasker >> 4 1576324 2.804613e-02 FALSE TRF Tandem Repeats Finder [period<=12] >> all masks together: >> maskedwidth maskedratio >> 26736688 0.4757021 >> all active masks together: >> maskedwidth maskedratio >> 150688 0.002681058 >> >> Cheers, >> H. >> >> >> Quoting Julie Zhu <julie.zhu at="" umassmed.edu="">: >> >>> Hi Herve, >>> >>> I need to obtain sequence data for a set of given coordinates. Do you know >>> whether Zv7 (zebrafish) sequence data will be made available for Bsgenome >>> package? Thanks! >>> >>> Best regards, >>> >>> Julie >>> >>> >>> ******************************************* >>> Julie Zhu, Ph.D >>> Research Assistant Professor >>> Program Gene Function and Expression >>> University of Massachusetts Medical School >>> 364 Plantation Street, Room 613 >>> Worcester, MA 01605 >>> 508-856-5256 >>> http://www.umassmed.edu/pgfe/faculty/zhu.cfm >>> >>> >>> >>> >> >> >> > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319