Docker image and Nextflow workflow quickly use the CALDER software for the analysis of Hi-C data.
This workflow uses the following docker image, containing all the dependencies required to execute it
Currently, the pipeline accepts a (list of) .hic files
nextflow run calder.nf --input path/to/hic/data.hic
| Parameter | Values | Description |
|---|---|---|
| --input | path (ex. ./data.hic) |
Path to .hic files. Can contain wildcards (*) |
| --chromosomes | "ALL" or a comma-separated list of chromosomes (ex. "1,2,3") | If "ALL", then all the chromosomes in the .hic file will be computed, otherwise only the ones provided in the list. (Default: "ALL") |
| --excludeChromosomes | Comma-separated list of chromosomes (ex. "1,2,3") | Excludes the specified chromosomes from the computation (Default: "Y,MT") |
| --binSize | Comma-separated list of resolutions (ex. "100000,250000") | Specifies at which resolutions the CALDER workflow should be performed. (Default: "100000") |
| --normalization | Comma-separated list of Hi-C normalization strategies (ex. "KR,VC") | Specifies which Hi-C normalizatios to use. (Default: "KR") |
| --out_dir | Path to the results folder (ex. "./results") | Specifies where to store the results of the analysis (Default: "results") |
The output of the workflow is stored in the folder specified by --out_dir ("results" by default) and will look like this:
results/
└── HiC_sample_1
├── 100000
│ └── KR
│ ├── chr1
│ │ ├── chr1_domain_boundaries.bed
│ │ ├── chr1_domain_hierachy.tsv
│ │ ├── chr1_log.txt
│ │ ├── chr1_nested_boundaries.bed
│ │ ├── chr1_sub_compartments.bed
│ │ └── chr1_sub_domains_log.txt
The specification of the output of CALDER is described in the respective repository.
If you use CALDER, this workflow or the relative Docker image in our research, please cite our paper:
- Liu, Y., Nanni, L., Sungalee, S. et al. Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes. Nat Commun 12, 2439 (2021). https://doi.org/10.1038/s41467-021-22666-3