Going forward

Look into

• Titus Brown and Colleague’s Next-Gen Sequence Analysis Workshops, most recent are Next-Gen Sequence Analysis Workshop (2014) and Next-Gen Sequence Analysis Workshop (2015). Particularly pertinent to today’s efforts 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 and here. However, there’s lots of stuff to be found there for those trying to get up and running in bioinformatics in general. And for those ready for more, see Titus’s coverage (chock full of links) of his week of classes offered first in 2015 for workshop alumni and advanced folks here.
• ChIP- and DNase-seq data analysis workshop 2014
• Cistrome - a web-based ChIP-seq analysis portal based on Galaxy open source framework run by the labs of Myles Brown and Xiaole Shirley Liu. It provides a complete workflow for ChIP-seq and downstram analysis without the need for local installation and configuration.
• A History of Bioinformatics (in the Year 2039), a presentation by Titus Brown encouraging good data practices in his unique way

Data Acquisition

• NCBI’s Sequence Read Archive (SRA) hosts a great deal of raw data.
• As described here, NCBI’s Gene Expression Omnibus (GEO) hosts processed forms of data and refers to the SRA for the raw data.
• European Nucleotide Archive (ENA) also hosts raw data but I found some select datasets slightly different from forms stored at SRA, i.e., split reads vs interleaved, etc..
• The Yeast Genome Database hosts a selection of curated datasets for S. cerevisiae here.

File Formats and Conversion help

• UCSC Genome Bioinformatics- Data File Formats FAQ section
• Data File format on Abecasis Group Wiki, for example SAM
• Ensembl’s documentation on file formats
• Bam2Wig example
• File Formats Listing associated with the Broad Institute’s Integrated Genomics Viewer

ChIP-seq data analysis

• 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 and here.
• ChIP-seq analysis using GALAXY: Part 1 - Introduction -uses MACS, CEAS, and WEEDER. The latter being an alternative to MEME for motif discovery.
• The ChIP-seq pipeline “Cistrome” integrated into UGENE uses MACS and CEAS and additional characterization of binding sites. You can read about it and the UGENE NGS platform here. The UGENE pipeline is originally based on the General ChIP-seq pipeline from the public Cistrome installation on the Galaxy workflow platform
• ChIP- and DNase-seq data analysis workshop 2014
• Cis-regulatory Element Annotation System by Hyunjin Shin and Tao Liu from Xiaole Shirley Liu’s Lab
• ab initio motif finder MEME and the related MEME suite
• MEME-LaB wraps the popular ab initio motif finder in a web tool
• Motif enrichment tool. Blatti C, Sinha S. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W20-5. doi: 10.1093/nar/gku456. Epub 2014 May 23. PMID: 24860165
• Motif-based analysis of large nucleotide data sets using MEME-ChIP

ChIP-exo methods

• Rhee HS and Pugh BF (2011) Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell 147(6):1408-19

• Several groups report good results and Illumina and other companies have kits and protocols

• Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties

• Webinar: “Precision Mapping”- High Resolution Mapping using ChIP-exo”

• No formaldehyde, no problem for new genome-wide ChIP method

  ORGANIC detected more Reb1 binding sites than either X-ChIP-chip or ChIP-exo.

Questions

• Try Google, probably will lead you to one of my listed resources or...
• Biostars
• Stackoverflow for general scripting and computing
• SEQanswers - a high throughput sequencing community
• Try Twitter - for example this