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Would it be possible to add version 10 of the zebrafish genome to BS genome.
Thank you so much
Neel
Would it be possible to add version 10 of the zebrafish genome to BS genome.
Thank you so much
Neel
Maybe the data in AnnotationHub are sufficient?
> library(AnnotationHub) > hub = AnnotationHub() snapshotDate(): 2015-07-17 > query(hub, "GRCz10") AnnotationHub with 8 records # snapshotDate(): 2015-07-17 # $dataprovider: Ensembl # $species: Danio rerio # $rdataclass: FaFile, GRanges # additional mcols(): taxonomyid, genome, description, tags, sourceurl, # sourcetype # retrieve records with, e.g., 'object[["AH47053"]]' title AH47053 | Danio_rerio.GRCz10.80.gtf AH47187 | Danio_rerio.GRCz10.cdna.all.fa AH47188 | Danio_rerio.GRCz10.dna_rm.toplevel.fa AH47189 | Danio_rerio.GRCz10.dna_sm.toplevel.fa AH47190 | Danio_rerio.GRCz10.dna.toplevel.fa AH47191 | Danio_rerio.GRCz10.ncrna.fa AH47192 | Danio_rerio.GRCz10.pep.all.fa AH47950 | Danio_rerio.GRCz10.81.gtf > dna = hub[["AH47190"]] > library(BSgenome) > seqinfo(dna) Seqinfo object with 1061 sequences from an unspecified genome: seqnames seqlengths isCircular genome 1 58871917 <NA> <NA> 10 45574255 <NA> <NA> 11 45107271 <NA> <NA> 12 49229541 <NA> <NA> 13 51780250 <NA> <NA> ... ... ... ... KN150481.1 1008 <NA> <NA> KN150657.1 1007 <NA> <NA> KN150461.1 1000 <NA> <NA> KN150247.1 728 <NA> <NA> KN150525.1 650 <NA> <NA> > getSeq(dna, GRanges(c("1", "10"), IRanges(1000000, width=1000))) A DNAStringSet instance of length 2 width seq names [1] 1000 CACAGCTGTCAGCATCCATTAAC...TATTATTATTATTATTGTGTTAT 1 [2] 1000 CCCACTAGTGCCCATCTATCCCT...NNNNNNNNNNNNNNNNNNNNNNN 10
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