Churros

Churros is a Docker-based epigenomics analysis pipeline. While Churros mainly focuses on the ChIP-seq analysis, it can also handle CUT&TAG, ATAC-seq and DNA methylation data.

Contents:

• 1. Installation
• 2. Quick start (ChIP-seq, human)
• 3. Quick start (ChIP-seq, S. cerevisiae)
• 4. Step-by-step analysis (ChIP-seq, human)
• 5. Spike-in analysis (human)
• 6. Peakheatmap: Large-scale profile analysis
• 7. DNA methylation analysis
• 8. ATAC-seq analysis
• 9. CUT&Tag/CUT&Run analysis
• 10. Commands in Churros

Citation:

• Wang J, Nakato R, Churros: a Docker-based pipeline for large-scale epigenomic analysis, DNA Research, 2023. doi: 10.1093/dnares/dsad026