Sources

The sources for the information used today came from those linked throughout the content.

However, certain sources deserve special highlighting as they were particularly useful in developing this presentation, contain a wealth of related resources, or are especially pertinent at this stage.

• README for MACS (2.1.0)
• Feng et al. 2012. Identifying ChIP-seq enrichment using MACS.Nat Protoc. 2012 Sep; 7(9): 10.1038/nprot.2012.101.
• Using MACS to Identify Peaks from ChIP-Seq Data. Curr Protoc Bioinformatics. 2011 Jun; CHAPTER: Unit2.14.
• • ChIP-Seq: technical considerations for obtaining high-quality data. Kidder BL, Hu G, Zhao K. Nat Immunol. 2011 Sep 20;12(10):918-22. doi: 10.1038/ni.2117. PMID: 21934668
• Titus Brown and Colleague’s Next-Gen Sequence Analysis Workshops, most recent is [Next-Gen Sequence Analysis Workshop (2014)(http://angus.readthedocs.org/en/2014/) Particularly pertinent are:
  • the sections Istvan Albert’s 2012 ChIP-Seq lecture
  • Day 7: ChIP-seq: Peak Predictions and Cis-regulatory Element Annotations* Using MEME to identify TF binding motif from ChIP-seq data * here.
  • For the mapping of the reads using bwa I relied heavily on Mapping reads with bwa and bowtie tutorial
  • Software packages to install
  • Another recent guide to software installation
• ChIP- and DNase-seq data analysis workshop 2014
• UCSC Genome Bioinformatics- Data File Formats FAQ section
• Rhee HS and Pugh BF (2011) Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell 147(6):1408-19