Package: BSgenome.Btaurus.UCSC.bosTau9
Title: Full genome sequences for Bos taurus (UCSC version bosTau9)
Description: Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau9, Apr. 2018) and stored in Biostrings objects.
Version: 1.4.2
Suggests: GenomicFeatures
organism: Bos taurus
common_name: Cow
provider: UCSC
provider_version: bosTau9
release_date: Apr. 2018
release_name: USDA ARS
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/bosTau9/bigZips/
organism_biocview: Bos_taurus
BSgenomeObjname: Btaurus
circ_seqs: "chrM"
SrcDataFiles: bosTau9.2bit from http://hgdownload.cse.ucsc.edu/goldenPath/bosTau9/bigZips/
PkgExamples: genome$chr1  # same as genome[["chr1"]]
	.
	## ---------------------------------------------------------------------
	## Extract the upstream sequences
	## ---------------------------------------------------------------------
	## The upstream sequences located in
	##   http://hgdownload.cse.ucsc.edu/goldenPath/bosTau9/bigZips/
	## are based on RefSeq genes (RefSeq Genes track in the Genome Browser).
	## These can easily be extracted from the full genome sequences with:
	.
	library(GenomicFeatures)
	refGene_txdb <- suppressWarnings(makeTxDbFromUCSC("bosTau9", "refGene"))
	refGene_up1000seqs <- extractUpstreamSeqs(genome, refGene_txdb)
	.
	## Note that you can make a TxDb object from various annotation
	## resources. See the makeTxDbFromUCSC(), makeTxDbFromEnsembl(), 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 bosTau9 or on a compatible genome
	## (i.e. a genome with sequences identical to the sequences in bosTau9).
	## See ?extractUpstreamSeqs in the GenomicFeatures package for more
	## information.
seqs_srcdir: /fh/fast/morgan_m/BioC/BSgenomeForge/srcdata/BSgenome.Btaurus.UCSC.bosTau9/seqs
seqfile_name: bosTau9.sorted.2bit