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Patterns and features on genomes in R: Biostrings, BSgenome and GenomicRanges.

'FLS' R group - October 2015

Dave Gerrard

Biostrings, BSgenomes and GenomicRanges.

PRE-REQUISITES --------------------------------

Multiple bioconductor packages but should get them all by doing this.

source("https://bioconductor.org/biocLite.R")
# Try http if https is not available
biocLite("BSgenome.Scerevisiae.UCSC.sacCer3")    
# 'should' also install Biostrings, BSgenomes and GenomicRanges if not already installed.

The Plan. --------------------------------------

Find instances of a DNA-sequence motif in a genome that also have evidence of binding from a ChIP-seq experiment.

  1. Biostrings
  2. BSgenome
  3. GenomicRanges

The tutorial is in the script BSgenome.BioStrings.bioC.R. You will need to download some data before you start (see below).

Data ---------------------------

Tutorial uses a table of genomic ChIP-seq peaks from Zheng et al., 2010, Nature

The data table GSE19635_s96a_peaks.txt was downloaded from GEO and uncompressed.