ChIP-Seq data analysis

ChIP-sequencing is a method used to analyze protein interactions with DNA.

Requirements

Before diving into this topic, we recommend you to have a look at:

• Introduction to Galaxy Analyses
• Sequence analysis
  • Quality Control: slides slides - tutorial hands-on
  • Mapping: slides slides - tutorial hands-on

Material

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

Maintainers

This material is maintained by:

Mallory Freeberg

Mo Heydarian

Friederike Dündar

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Bérénice Batut

Friederike Dündar

Anika Erxleben

Vivek Bhardwaj

Fidel Ramirez

Leily Rabbani

Mallory Freeberg

Mo Heydarian

Joachim Wolff

References

• Stephen G Landt et al: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
  A very useful encyclopedic paper with many details about the tools the (mod)ENCODE consortia use and also contains a long section about antibody validation
• Gabriel E Zentner and Steven Henikoff: Surveying the epigenomic landscape, one base at a time
  Overview of popular sequencing techniques with very nice descriptions of DNase-seq, MNase-seq, FAIRE-seq
• Benjamin L Kidder et al: ChIP-Seq: technical considerations for obtaining high-quality data
  Nice, readable introduction into all aspects of ChIP-seq experiments (from antibodies to cell numbers to replicates to data analysis)
• Marion Leleu et al: Processing and analyzing ChIP-seq data
  Fairly detailed review of key concepts of ChIP-seq data processing (less detailed on analysis)
• Peter J. Park: ChIP-seq: Advantages and challenges of a maturing technology
• Peter V Kharchenko et al: Design and analysis of ChIP-seq experiments for DNA-binding proteins
• Edison T Liu et al: Q&A: ChIP-seq technologies and the study of gene regulation
  Short overview of several (typical) issues of ChIP-seq analysis
• Thomas S. Carroll et al: Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data
• Shirley Pepke et al: Computation for ChIP-seq and RNA-seq studies
  First comparison of peak callers, focuses on the explanation of basic principles of ChIP-seq data processing and general workflows of peak calling algorithms
• Elizabeth G. Wilbanks & Marc T. Facciotti: Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
  Another comparison of peak callers - focuses more on the evaluation of the peak callers performances than Shirley Pepke et al.
• Mariann Micsinai et al: Picking ChIP-seq peak detectors for analyzing chromatin modification experiments
  'How to choose the best peak caller for your data set - their finding: default parameters, surprisingly, yield the most reproducible results regardless of the data set type'
• Jianxing Fen et al: Identifying ChIP-seq enrichment using MACS
  How to use MACS
• Yong Zhang et al: Model-based Analysis of ChIP-Seq (MACS)
  Original publication of MACS
• Modan K Das & Ho-Kwok Dai: A survey of DNA motif finding algorithms
  Review of motif analysis tools
• Philip Machanick and Timothy L. Bailey: MEME-ChIP: motif analysis of large DNA datasets
  MEME-ChIP-paper
• Timothy L. Bailey and Philip Machanick: Inferring direct DNA binding from ChIP-seq
  'Centrimo: position-specific motif analysis, especially useful for ChIP-seq data'
• Morgane Thomas-Chollier et al: Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs
  How to use TRAP
• Helge G. Roider et al: Predicting transcription factor affinities to DNA from a biophysical model
  Theoretical background of TRAP