Chromatin immunoprecipitation (ChIP) is a powerful workflow for analysis of chromatin structure. The antibody-based pulled down of protein-DNA interactions is only half the process. Once the genomic regions bound by a protein are enriched and sequenced, bioinformatics tools and pipelines are necessary to identify, characterize, and compare these regions between samples.
This ‘dry’ side of the ChIP workflow is as important as the ‘wet’, and has much more flexibility. This means that the researcher’s dry workflow choices have a big impact on the experimental outcome.
Three key stages of bioinformatics analysis are required. Inside this eBook we review these stages and highlight useful tools for each.
- Peak Calling and Statistical Analysis Tools
- Browsing and Visualization Applications
- Databases and Motif Finding