BSgenome Sscrofa 11.1
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MartaG • 0
@martag-13812
Last seen 4.1 years ago

Dear Herve,

I would like to kindly request the new pig genome (Sscrofa 11.1) for the BSgenome package. It is not yet in UCSC but it is in Ensembl (http://www.ensembl.org/Sus_scrofa/Info/Index). I do not need the masked version though.

Thanks in advance,

Marta

sus scrofa bsgenome • 1.2k views
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@martin-morgan-1513
Last seen 10 weeks ago
United States

Maybe the resources in AnnotationHub are enough for your purposes?

> library(AnnotationHub)
> hub = AnnotationHub()
snapshotDate(): 2017-07-11
> query(hub, c("release-89", "Sus"))
AnnotationHub with 7 records
# snapshotDate(): 2017-07-11 
# $dataprovider: Ensembl
# $species: Sus scrofa
# $rdataclass: TwoBitFile, GRanges
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH55359"]]' 

            title                                      
  AH55359 | Sus_scrofa.Sscrofa10.2.89.abinitio.gtf     
  AH55360 | Sus_scrofa.Sscrofa10.2.89.chr.gtf          
  AH55361 | Sus_scrofa.Sscrofa10.2.89.gtf              
  AH55697 | Sus_scrofa.Sscrofa10.2.cdna.all.2bit       
  AH55698 | Sus_scrofa.Sscrofa10.2.dna_rm.toplevel.2bit
  AH55699 | Sus_scrofa.Sscrofa10.2.dna_sm.toplevel.2bit
  AH55700 | Sus_scrofa.Sscrofa10.2.ncrna.2bit          
> dna = hub[["AH55698"]]  ## download first time; reload from cache subsequently
loading from cache '/home/mtmorgan//.AnnotationHub/62436'
> getSeq(dna, GRanges("10:1000000-20000000"))
  A DNAStringSet instance of length 1
       width seq
[1] 19000001 CCTTCTAACTGAAAGAATTGAAGAATATTCAA...CANNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
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Hi, is not working for me. The only available dataset is Sus_scrofa.Sscrofa10.2 (v.89) but I would like the Sus_scrofa.Sscrofa11.1 (v.90), relased last week.

 

This is the output that I get with the R v.3.4.1 with "query(hub, c("Sus"))" :

AnnotationHub with 150 records

# snapshotDate(): 2017-04-25 
# $dataprovider: Ensembl, UCSC, Inparanoid8
# $species: Sus scrofa
# $rdataclass: FaFile, GRanges, TwoBitFile, ChainFile, Inparanoid8Db
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded,
#   preparerclass, tags, rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH307"]]' 

            title                                       
  AH307   | Sus_scrofa.Sscrofa10.2.69.cdna.all.fa       
  AH308   | Sus_scrofa.Sscrofa10.2.69.dna.toplevel.fa   
  AH309   | Sus_scrofa.Sscrofa10.2.69.dna_rm.toplevel.fa
  AH310   | Sus_scrofa.Sscrofa10.2.69.dna_sm.toplevel.fa
  AH311   | Sus_scrofa.Sscrofa10.2.69.ncrna.fa          
  ...       ...                                         
  AH51411 | Sus_scrofa.Sscrofa10.2.cdna.all.2bit        
  AH51412 | Sus_scrofa.Sscrofa10.2.dna_rm.toplevel.2bit 
  AH51413 | Sus_scrofa.Sscrofa10.2.dna_sm.toplevel.2bit 
  AH51414 | Sus_scrofa.Sscrofa10.2.dna.toplevel.2bit    
  AH51415 | Sus_scrofa.Sscrofa10.2.ncrna.2bit

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Try updating to use the devel version of Biocoductor, where release 90 is now available.

> library(AnnotationHub)
> hub = AnnotationHub()
snapshotDate(): 2017-08-28
> query(hub, c("Sus_scr", "90"))
AnnotationHub with 7 records
# snapshotDate(): 2017-08-28 
# $dataprovider: Ensembl
# $species: Sus scrofa
# $rdataclass: TwoBitFile, GRanges
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH57293"]]' 

            title                                      
  AH57293 | Sus_scrofa.Sscrofa11.1.90.abinitio.gtf     
  AH57294 | Sus_scrofa.Sscrofa11.1.90.chr.gtf          
  AH57295 | Sus_scrofa.Sscrofa11.1.90.gtf              
  AH57691 | Sus_scrofa.Sscrofa11.1.cdna.all.2bit       
  AH57692 | Sus_scrofa.Sscrofa11.1.dna_rm.toplevel.2bit
  AH57693 | Sus_scrofa.Sscrofa11.1.dna_sm.toplevel.2bit
  AH57694 | Sus_scrofa.Sscrofa11.1.ncrna.2bit          
> dna = hub[["AH57692"]]
require("rtracklayer")
downloading from 'https://annotationhub.bioconductor.org/fetch/64430'
retrieving 1 resource
  |======================================================================| 100%
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