And there is this for your build: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/ On Mon, Jul 14, 2014 at 10:06 AM, James W. MacDonald <jmacdon@uw.edu> wrote: > This may help clear things up for you: > > http://genome.ucsc.edu/FAQ/FAQdownloads.html#download9 > > Best, > > Jim > > > > > On 7/14/2014 5:03 AM, Asma rabe wrote: > >> Hi All, >> >> When I tried BSgenome package for Hsapiens I got the output below. I >> wonder >> what are chromosomes other than chr1-chr22,chrX,Y and M. >> What is chr4_gl000193_random for instance. >> >> Thank you >> #========= >> >> Hsapiens >> Human genome >> | >> | organism: Homo sapiens (Human) >> | provider: UCSC >> | provider version: hg19 >> | release date: Feb. 2009 >> | release name: Genome Reference Consortium GRCh37 >> | >> | single sequences (see '?seqnames'): >> | chr1 chr2 chr3 >> chr4 chr5 >> | chr6 chr7 chr8 >> chr9 chr10 >> | chr11 chr12 chr13 >> chr14 chr15 >> | chr16 chr17 chr18 >> chr19 chr20 >> | chr21 chr22 chrX >> chrY chrM >> | chr1_gl000191_random chr1_gl000192_random chr4_ctg9_hap1 >> chr4_gl000193_random chr4_gl000194_random >> | chr6_apd_hap1 chr6_cox_hap2 chr6_dbb_hap3 >> chr6_mann_hap4 chr6_mcf_hap5 >> | chr6_qbl_hap6 chr6_ssto_hap7 chr7_gl000195_random >> chr8_gl000196_random chr8_gl000197_random >> | chr9_gl000198_random chr9_gl000199_random chr9_gl000200_random >> chr9_gl000201_random chr11_gl000202_random >> | chr17_ctg5_hap1 chr17_gl000203_random chr17_gl000204_random >> chr17_gl000205_random chr17_gl000206_random >> | chr18_gl000207_random chr19_gl000208_random chr19_gl000209_random >> chr21_gl000210_random chrUn_gl000211 >> | chrUn_gl000212 chrUn_gl000213 chrUn_gl000214 >> chrUn_gl000215 chrUn_gl000216 >> | chrUn_gl000217 chrUn_gl000218 chrUn_gl000219 >> chrUn_gl000220 chrUn_gl000221 >> | chrUn_gl000222 chrUn_gl000223 chrUn_gl000224 >> chrUn_gl000225 chrUn_gl000226 >> | chrUn_gl000227 chrUn_gl000228 chrUn_gl000229 >> chrUn_gl000230 chrUn_gl000231 >> | chrUn_gl000232 chrUn_gl000233 chrUn_gl000234 >> chrUn_gl000235 chrUn_gl000236 >> | chrUn_gl000237 chrUn_gl000238 chrUn_gl000239 >> chrUn_gl000240 chrUn_gl000241 >> | chrUn_gl000242 chrUn_gl000243 chrUn_gl000244 >> chrUn_gl000245 chrUn_gl000246 >> | chrUn_gl000247 chrUn_gl000248 chrUn_gl000249 >> | >> | multiple sequences (see '?mseqnames'): >> | upstream1000 upstream2000 upstream5000 >> | >> | (use the '$' or '[[' operator to access a given sequence) >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> >> > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane. > science.biology.informatics.conductor > -- Brian Herb, Ph.D. Johns Hopkins School of Medicine Dr. Andrew Feinberg Laboratory Rangos 580 855 N. Wolfe St. Baltimore, MD 21205 Phone:410-614-3478 Fax: 410-614-9819 [[alternative HTML version deleted]]