Package: BSgenome.Hsapiens.UCSC.hg19
Title: Full genome sequences for Homo sapiens (UCSC version hg19)
Description: Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects.
Version: 1.4.2
Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene
organism: Homo sapiens
common_name: Human
provider: UCSC
provider_version: hg19
release_date: Feb. 2009
release_name: Genome Reference Consortium GRCh37
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
organism_biocview: Homo_sapiens
BSgenomeObjname: Hsapiens
seqnames: paste("chr", c(1:22, "X", "Y", "M", "1_gl000191_random", "1_gl000192_random", "4_ctg9_hap1", "4_gl000193_random", "4_gl000194_random", "6_apd_hap1", "6_cox_hap2", "6_dbb_hap3", "6_mann_hap4", "6_mcf_hap5", "6_qbl_hap6", "6_ssto_hap7", "7_gl000195_random" , "8_gl000196_random", "8_gl000197_random", "9_gl000198_random", "9_gl000199_random", "9_gl000200_random", "9_gl000201_random", "11_gl000202_random", "17_ctg5_hap1", "17_gl000203_random", "17_gl000204_random", "17_gl000205_random", "17_gl000206_random", "18_gl000207_random", "19_gl000208_random", "19_gl000209_random", "21_gl000210_random", paste("Un_gl000", 211:249, sep="")), sep="")
circ_seqs: "chrM"
SrcDataFiles: chromFa.zip from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
PkgExamples: genome$chr1  # same as genome[["chr1"]]
	.
	## ---------------------------------------------------------------------
	## Upstream sequences
	## ---------------------------------------------------------------------
	## Starting with BioC 3.0, the upstream1000, upstream2000, and
	## upstream5000 sequences for hg19 are not included in the BSgenome data
	## package anymore. However they can easily be extracted from the full
	## genome sequences with something like:
	.
	library(TxDb.Hsapiens.UCSC.hg19.knownGene)
	txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
	gn <- sort(genes(txdb))
	up1000 <- flank(gn, width=1000)
	up1000seqs <- getSeq(genome, up1000)
	.
	## IMPORTANT: Make sure you use a TxDb package (or TxDb object),
	## that contains a gene model based on the exact same reference genome
	## as the BSgenome object you pass to getSeq(). Note that you can make
	## your own custom TxDb object from various annotation resources.
	## See the makeTxDbFromUCSC(), makeTxDbFromBiomart(),
	## and makeTxDbFromGFF() functions in the GenomicFeatures
	## package.
seqs_srcdir: /fh/fast/morgan_m/BioC/BSgenomeForge/srcdata/BSgenome.Hsapiens.UCSC.hg19/seqs