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.
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"))" :
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.