Hi Herve, Thank you for the clarification. Cheers, Diego On Tue, Nov 5, 2013 at 4:01 PM, Hervé Pagès <hpages at="" fhcrc.org=""> wrote: > Hi Diego, > > > On 11/04/2013 09:35 PM, Diego Diez wrote: >> >> Dear all, >> >> I have noticed that BSgenome.Mmusculus.UCSC.mm10 does not contain >> entries for upstream sequences (upstream1000, upstream2000, >> upstream5000) like for example BSgenome.Mmusculus.UCSC.mm9 does (see >> bellow). Is there a reason for this? > > > Could be that I forgot, or that it was on purpose, I can't remember. > The plan is to deprecate the upstream sequences in BioC 2.14 and > to remove them in BioC 2.15. This is because now we have > getPromoterSeq() in the GenomicFeatures package, which is more > flexible. > > Cheers, > H. > >> >> Thank you, >> Diego >> >> >>> library(BSgenome.Mmusculus.UCSC.mm9) >>> Mmusculus >> >> Mouse genome >> | >> | organism: Mus musculus (Mouse) >> | provider: UCSC >> | provider version: mm9 >> | release date: Jul. 2007 >> | release name: NCBI Build 37 >> | >> | single sequences (see '?seqnames'): >> | chr1 chr2 chr3 chr4 chr5 >> | chr6 chr7 chr8 chr9 chr10 >> | chr11 chr12 chr13 chr14 chr15 >> | chr16 chr17 chr18 chr19 chrX >> | chrY chrM chr1_random chr3_random chr4_random >> | chr5_random chr7_random chr8_random chr9_random chr13_random >> | chr16_random chr17_random chrX_random chrY_random chrUn_random >> | >> | multiple sequences (see '?mseqnames'): >> | upstream1000 upstream2000 upstream5000 >> | >> | (use the '$' or '[[' operator to access a given sequence) >> >> >> >> library(BSgenome.Mmusculus.UCSC.mm10) >> Mmusculus >> Mouse genome >> | >> | organism: Mus musculus (Mouse) >> | provider: UCSC >> | provider version: mm10 >> | release date: Dec. 2011 >> | release name: Genome Reference Consortium GRCm38 >> | >> | sequences (see '?seqnames'): >> | chr1 chr2 chr3 >> | chr4 chr5 chr6 >> | chr7 chr8 chr9 >> | chr10 chr11 chr12 >> | chr13 chr14 chr15 >> | chr16 chr17 chr18 >> | chr19 chrX chrY >> | chrM chr1_GL456210_random chr1_GL456211_random >> | chr1_GL456212_random chr1_GL456213_random chr1_GL456221_random >> | chr4_GL456216_random chr4_GL456350_random chr4_JH584292_random >> | chr4_JH584293_random chr4_JH584294_random chr4_JH584295_random >> | chr5_GL456354_random chr5_JH584296_random chr5_JH584297_random >> | chr5_JH584298_random chr5_JH584299_random chr7_GL456219_random >> | chrX_GL456233_random chrY_JH584300_random chrY_JH584301_random >> | chrY_JH584302_random chrY_JH584303_random chrUn_GL456239 >> | chrUn_GL456359 chrUn_GL456360 chrUn_GL456366 >> | chrUn_GL456367 chrUn_GL456368 chrUn_GL456370 >> | chrUn_GL456372 chrUn_GL456378 chrUn_GL456379 >> | chrUn_GL456381 chrUn_GL456382 chrUn_GL456383 >> | chrUn_GL456385 chrUn_GL456387 chrUn_GL456389 >> | chrUn_GL456390 chrUn_GL456392 chrUn_GL456393 >> | chrUn_GL456394 chrUn_GL456396 chrUn_JH584304 >> | >> | (use the '$' or '[[' operator to access a given sequence) >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319