Elementolab/ChIPseeqer Tutorial

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	* Analysis 5: Evaluate conservation of detected peaks		* Analysis 5: Evaluate conservation of detected peaks
-	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_2Cons Use Use ChIPseeqer2Cons]	+	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_2Cons Use ChIPseeqer2Cons]
	* Analysis 6: Comparing detected peaks between datasets		* Analysis 6: Comparing detected peaks between datasets
-	** Use Compare Intervals	+	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Compare_Intervals Use Compare Intervals]
	* Analysis 7: Comparing RefSeq genes between datasets		* Analysis 7: Comparing RefSeq genes between datasets
	** Use Compare Genes		** Use Compare Genes

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Revision as of 02:43, 29 October 2009

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: Search for regulatory elements using FIRE
  • Use ChIPseeqer2FIRE

• Analysis 4: Determine pathways associated with genes using iPAGE
  • Use ChIPseeqer2iPAGE

• Analysis 5: Evaluate conservation of detected peaks
  • Use ChIPseeqer2Cons

• Analysis 6: Comparing detected peaks between datasets
  • Use Compare Intervals

• Analysis 7: Comparing RefSeq genes between datasets
  • Use Compare Genes