nf-chicago

Pipeline for detection of DNA looping interactions in capture Hi-C data

nf-chicago is a pipeline for calling DNA looping interactions in capture Hi-C/Micro-C data using CHiCAGO (Capture Hi-C Analysis of Genomic Organisation) library. CHiCAGO compatible bam files are required to run this workflow.

The workflow and scripts here are based on this Dovetail tutorial about data analysis for promoter capture on Hi-C libraries using RE-free methods (Omni-C® or Micro-C® assays) . Check the tutorial for more details about how to prepare required input files, including CHiCAGO compatible bam files. You can use this pipeline to generate CHiCAGO compatible bam.

Usage

nextflow run dhslab/nf-chicago -r main -latest \
-profile YOURPROFILE(S) \
--input <SAMPLESHEET> \
--design_directory <DESIGN_DIRECTORY> \
--rmap <DIGEST_MAP_FILE> \
--baitmap <BAITMAP_FILE> \
--outdir <OUTDIR> 

Directory tree for run output:

.
├── test1
│   ├── chicago_calls
│   │   ├── data
│   │   │   ├── test1.Rds
│   │   │   ├── test1.bedpe
│   │   │   ├── test1.ibed
│   │   │   └── test1_params.txt
│   │   ├── diag_plots
│   │   │   ├── test1_distFun.pdf
│   │   │   ├── test1_oeNorm.pdf
│   │   │   └── test1_techNoise.pdf
│   │   ├── enrichment_data
│   │   └── examples
│   │       └── test1_proxExamples.pdf
│   └── preprocessing
│       ├── test1.chinput
│       └── test1_bait2bait.bedpe
└── test2
    ├── chicago_calls
    │   ├── data
    │   │   ├── test2.Rds
    │   │   ├── test2.bedpe
    │   │   ├── test2.ibed
    │   │   └── test2_params.txt
    │   ├── diag_plots
    │   │   ├── test2_distFun.pdf
    │   │   ├── test2_oeNorm.pdf
    │   │   └── test2_techNoise.pdf
    │   ├── enrichment_data
    │   └── examples
    │       └── test2_proxExamples.pdf
    └── preprocessing
        ├── test2.chinput
        └── test2_bait2bait.bedpe