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
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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version 2.3.6
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
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%