Package: BSgenome.Mmulatta.UCSC.rheMac3 Title: Full genome sequences for Macaca mulatta (UCSC version rheMac3) Description: Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects. Version: 1.4.2 Suggests: GenomicFeatures organism: Macaca mulatta common_name: Rhesus provider: UCSC provider_version: rheMac3 release_date: Oct. 2010 release_name: Beijing Genomics Institute CR_1.0 source_url: http://hgdownload.soe.ucsc.edu/goldenPath/rheMac3/ organism_biocview: Macaca_mulatta BSgenomeObjname: Mmulatta seqnames: paste("chr", c(1:20, "X", "M"), sep="") circ_seqs: "chrM" mseqnames: "chrUn" SrcDataFiles: rheMac3.fa.gz from http://hgdownload.soe.ucsc.edu/goldenPath/rheMac3/bigZips/ PkgExamples: genome$chr1 # same as genome[["chr1"]] . ## --------------------------------------------------------------------- ## Upstream sequences ## --------------------------------------------------------------------- ## Starting with BioC 3.0, the upstream1000, upstream2000, and ## upstream5000 sequences for rheMac3 are not included in the BSgenome ## data package anymore. However they can easily be extracted from the ## full genome sequences with something like: . library(GenomicFeatures) txdb <- makeTxDbFromUCSC("rheMac3", "refGene") 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.Mmulatta.UCSC.rheMac3/seqs