ChIP-Seq data analysis
ChIP-sequencing is a method used to analyze protein interactions with DNA.
Before diving into this topic, we recommend you to have a look at:
- Introduction to Galaxy Analyses
- Sequence analysis
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Introduction to ChIP-Seq data analysis
Formation of the Super-Structures on the Inactive X
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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.
This material is maintained by:Mo Heydarian, Friederike Dündar
For any question related to this topic and the content, you can contact them or visit our Gitter channel.
This material was contributed to by:Bérénice Batut, Friederike Dündar, Anika Erxleben, Vivek Bhardwaj, Fidel Ramirez, Leily Rabbani, Mallory Freeberg, Mo Heydarian, Joachim Wolff
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
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