Package: BSgenome.Drerio.UCSC.danRer11
Title: Full genome sequences for Danio rerio (UCSC version danRer11)
Description: Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.
Version: 1.4.2
Suggests: GenomicFeatures
organism: Danio rerio
common_name: Zebrafish
provider: UCSC
provider_version: danRer11
release_date: May 2017
release_name: Genome Reference Consortium GRCz11
source_url: http://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/
organism_biocview: Danio_rerio
BSgenomeObjname: Drerio
circ_seqs: "chrM"
SrcDataFiles: danRer11.2bit from http://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/
PkgExamples: genome$chr1  # same as genome[["chr1"]]
	.
	## ---------------------------------------------------------------------
	## Extract the upstream sequences
	## ---------------------------------------------------------------------
	## The upstream sequences located in
	##   http://hgdownload.cse.ucsc.edu/goldenPath/danRer11/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("danRer11", "refGene"))
	refGene_up1000seqs <- extractUpstreamSeqs(genome, refGene_txdb)
	.
	## Note that you can make TxDb objects 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 danRer11 or on a compatible genome
	## (i.e. a genome with sequences identical to the sequences in
	## danRer11). See ?extractUpstreamSeqs in the GenomicFeatures package
	## for more information.
seqs_srcdir: /fh/fast/morgan_m/BioC/BSgenomeForge/srcdata/BSgenome.Drerio.UCSC.danRer11/seqs
seqfile_name: danRer11.sorted.2bit