[BioC] Bsgenome Zv7 sequence data

[Julie Zhu]

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 ŒBSgenome.Drerio.UCSC.danRer5¹ 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...GGAGGATCTGACGTCTGTGAGCAAACACAAACACAC
> 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
>> 
>> 
>> 
>> 
> 
> 
> 
>