Package: BSgenome.Hsapiens.UCSC.hg38
Title: Full genome sequences for Homo sapiens (UCSC version hg38)
Description: Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.
Version: 1.4.2
Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene
organism: Homo sapiens
common_name: Human
provider: UCSC
provider_version: hg38
release_date: Dec. 2013
release_name: Genome Reference Consortium GRCh38
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/
organism_biocview: Homo_sapiens
BSgenomeObjname: Hsapiens
circ_seqs: "chrM"
SrcDataFiles: hg38.2bit from http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/
PkgExamples: genome$chr1  # same as genome[["chr1"]]
	.
	## ---------------------------------------------------------------------
	## Extract the upstream sequences
	## ---------------------------------------------------------------------
	## The upstream sequences located in
	##   http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/
	## are based on RefSeq genes (RefSeq Genes track in the Genome Browser).
	## Upstream sequences based on UCSC genes (UCSC Genes track in the
	## Genome Browser) can easily be extracted from the full genome
	## sequences with:
	.
	library(TxDb.Hsapiens.UCSC.hg38.knownGene)
	knownGene_txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
	knownGene_up1000seqs <- extractUpstreamSeqs(genome, knownGene_txdb)
	.
	## Or, to get upstream sequences based on RefSeq genes:
	.
	refGene_txdb <- makeTxDbFromUCSC("hg38", "refGene")
	refGene_up1000seqs <- extractUpstreamSeqs(genome, refGene_txdb)
	.
	## Note that you can make a TxDb object from various annotation
	## resources. See the makeTxDbFromUCSC(), makeTxDbFromBiomart(), and
	## makeTxDbFromGFF() functions in the GenomicFeatures package for more
	## information.
	## IMPORTANT: Make sure you use a TxDb package (or TxDb object) that
	## contains a gene model based on hg38 or on a compatible genome (i.e.
	## a genome with sequences identical to the sequences in hg38). See
	## ?extractUpstreamSeqs in the GenomicFeatures package for more
	## information.
seqs_srcdir: /fh/fast/morgan_m/BioC/BSgenomeForge/srcdata/BSgenome.Hsapiens.UCSC.hg38/seqs
seqfile_name: hg38.sorted.2bit