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@@ -147,6 +147,23 @@ CALDER_sub_domains(intermediate_data_file,
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* log file storing the status and running time of each step
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+## Output Structure
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+The output of the workflow is stored in the folder specified by `--out_dir` ("results" by default) and will look like this:
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+```
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+results/
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+└── HiC_sample_1
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+ ├── 100000
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+ │ └── KR
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+ │ ├── chr1
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+ │ │ ├── chr1_domain_boundaries.bed
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+ │ │ ├── chr1_domain_hierachy.tsv
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+ │ │ ├── chr1_log.txt
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+ │ │ ├── chr1_nested_boundaries.bed
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+ │ │ ├── chr1_sub_compartments.bed
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+ │ │ └── chr1_sub_domains_log.txt
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+
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+```
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+
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### Runnig time:
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For the computational requirement, running CALDER on the GM12878 Hi-C dataset at bin size of 40kb took **36 minutes** to derive the chromatin domains and their hierarchy for all chromosomes (i.e., CALDER Step1 and Step2); **13 minutes** to derive the nested sub-domains (i.e., CALDER Step3). At the bin size of 10kb, it took **1 h 44 minutes and 55 minutes** correspondingly (server information: 40 cores, 64GB Ram, Intel(R) Xeon(R) Silver 4210 CPU @ 2.20GHz). The evaluation was done using a single core although CALDER can be run in a parallel manner.
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Yuanlong LIU