[BioC] Bsgenome Zv7 sequence data

[Hervé Pagès]

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

-- 
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
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