What is ChIP-seq?

ChIP-seq with Bioconductor in R

Peter Humburg

Statistician, Macquarie University

ChIP-seq with Bioconductor in R

ChIP-seq with Bioconductor in R

ChIP-seq with Bioconductor in R

ChIP-seq with Bioconductor in R

ChIP-seq with Bioconductor in R

The Data

  • Prostate cancer patients
    • 5 primary tumor samples
    • 3 treatment resistant samples
  • ChIP targetting Androgen Receptor
  • AR is activated by binding testosterone
  • Activated AR regulates gene expression of target genes
ChIP-seq with Bioconductor in R

Accessing ChIP-seq data in R

  • Loading BAM files
library(GenomicAlignments)
reads <- readGAlignments('file_name')
  • Obtaining read coordinates
seqnames(reads)
start(reads)
end(reads)
  • Computing coverage
coverage(reads)
ChIP-seq with Bioconductor in R

Accessing peak calls

  • Loading BED files
library(rtracklayer)
peaks <- import.bed('file_name')
  • Obtaining peak coordinates
chrom(peaks)
ranges(peaks)
  • Extracting peak scores
score(peaks)
ChIP-seq with Bioconductor in R

Let's practice!

ChIP-seq with Bioconductor in R

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