Elementolab/ChIPseeqer Tutorial

From Icbwiki

ChIPseeqer TUTORIAL

This is a comprehensive step-by-step tutorial on how to use the ChIPseeqer tools to analyze ChIP-seq data.

• Analysis 1: Peak detection
  • Split raw data
  • Use ChIPseeqer
  • Use ChIPseeqerSummary

• Analysis 2: Visualize peak locations in UCSC Genome Browser
  • Use ChIPseeqer2Track

• Analysis 3: Smooth read counts across the whole genome (or across a given interval or sets of intervals) and creates a read density track for the UCSC Genome Browser
  • Use ChIPsmoothedReads2Track

• Analysis 4: Search for regulatory elements using FIRE
  • Use ChIPseeqer2FIRE

• Analysis 5: Determine pathways associated with genes using iPAGE
  • Use ChIPseeqer2iPAGE

• Analysis 6: Evaluate conservation of detected peaks
  • Use ChIPseeqer2Cons

• Analysis 7: Comparing detected peaks between datasets
  • Use Compare Intervals

• Analysis 8: Comparing RefSeq genes between datasets
  • Use Compare Genes

• Analysis 9: Annotate and filter the detected peaks (Repeating elements-RepMasker, CpG islands, Segmental Duplications)
  • Use ChIPseeqerAnnotate