Elementolab/ChIPseeqer Tutorial

From Icbwiki

Revision as of 04:52, 29 October 2009 Ole2001 (Talk | contribs) ← Previous diff		Revision as of 02:39, 6 November 2009 Ole2001 (Talk | contribs) Next diff →
Line 26:		Line 26:
	* Analysis 7: Comparing RefSeq genes between datasets		* Analysis 7: Comparing RefSeq genes between datasets
	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Compare_Genes Use Compare Genes]		** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Compare_Genes Use Compare Genes]
		+
		+	* Analysis 8: Annotate and filter the detected peaks (Repeating elements-RepMasker, CpG islands, Segmental Duplications)
		+	** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_Annotate Use ChIPseeqerAnnotate]

---

Revision as of 02:39, 6 November 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

• Analysis 8: Annotate and filter the detected peaks (Repeating elements-RepMasker, CpG islands, Segmental Duplications)
  • Use ChIPseeqerAnnotate