Hi Herve, Thank you very much! Best regards, Julie On 7/28/09 12:49 PM, "Hervé Pagès" <hpages at="" fhcrc.org=""> wrote: > Hi Julie, > > Julie Zhu wrote: >> 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! > > I'll try to build a BSgenome data package for zebrafish today and will let > you know when it's ready. > > Cheers, > H. > >> >> 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi Herve, Thank you very much! Best regards, Julie 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...GGAGGATCTGACGTCTGTGAGCAAACACA AACACAC > 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 >> >> >> >> > > > >

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 > 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...GGAGGATCTGACGTCTGTGAGCAAACACA AACACAC > 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 >> >> >> >> > > > >