danRer10 BSgenome file
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@chen_xuepeng-8344
Last seen 8.7 years ago

Version danRer10 for zebrafish genome in UCSC has been published for a while. our core team or big god can update it? that will be awesome 

genomicfeatures • 732 views
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@james-w-macdonald-5106
Last seen 2 hours ago
United States

Sooner or later the packaged annotation data will go away, and you will need to use AnnotationHub to get things you want.

> library(AnnotationHub)
> hub <- AnnotationHub()

> dr <- query(hub, c("Danio rerio"))

> grep("GRCz10", mcols(dr)$title, value = TRUE)
[1] "Danio_rerio.GRCz10.80.gtf"           
[2] "Danio_rerio.GRCz10.cdna.all.fa"      
[3] "Danio_rerio.GRCz10.dna_rm.toplevel.fa"
[4] "Danio_rerio.GRCz10.dna_sm.toplevel.fa"
[5] "Danio_rerio.GRCz10.dna.toplevel.fa"  
[6] "Danio_rerio.GRCz10.ncrna.fa"         
[7] "Danio_rerio.GRCz10.pep.all.fa"        

> dr.fa <- dr[["Danio_rerio.GRCz10.dna.toplevel.fa"]]
retrieving 2 resources
  |======================================================================| 100%
  |======================================================================| 100%

> library(Rsamtools)

> scanFa(dr.fa, GRanges("1", IRanges(1,500)))
  A DNAStringSet instance of length 1
    width seq                                               names              
[1]   500 GATCTTAAACATTTATTCCCCCT...TCTGCATAGAGCACACAAGTATG 1

> scanFa(dr.fa, GRanges(c("1","2"), IRanges(c(1,600), c(500, 1250))))
  A DNAStringSet instance of length 2
    width seq                                               names               
[1]   500 GATCTTAAACATTTATTCCCCCT...TCTGCATAGAGCACACAAGTATG 1
[2]   651 TTAAGTTTGAGGGAAGGTTGTTA...GGATCATATTTGCTGCTATTTTT 2

 

 

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