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@@ -253,18 +253,42 @@ CALDER(contact_file_dump=contact_file_dump,
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## Output Structure
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The output of the workflow is stored in the folder specified by `--save_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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+CALDER_dev_output/
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+|-- [ 37] intermediate_data
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+| `-- [ 56] sub_compartments
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+| |-- [ 4.0K] 100kb
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+| | |-- [ 2.6K] chr21_domain_boundaries.bed
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+| | |-- [ 2.1K] chr21_domain_hierachy.tsv
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+| | |-- [ 518] chr21_log.txt
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+| | |-- [ 3.4K] chr21_sub_compartments.bed
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+| | |-- [ 2.7K] chr22_domain_boundaries.bed
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+| | |-- [ 2.2K] chr22_domain_hierachy.tsv
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+| | |-- [ 517] chr22_log.txt
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+| | `-- [ 3.5K] chr22_sub_compartments.bed
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+| |-- [ 4.0K] 10kb
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+| | |-- [ 13K] chr21_domain_boundaries.bed
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+| | |-- [ 11K] chr21_domain_hierachy.tsv
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+| | |-- [ 494] chr21_log.txt
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+| | |-- [ 18K] chr21_sub_compartments.bed
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+| | |-- [ 15K] chr22_domain_boundaries.bed
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+| | |-- [ 13K] chr22_domain_hierachy.tsv
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+| | |-- [ 494] chr22_log.txt
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+| | `-- [ 21K] chr22_sub_compartments.bed
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+| `-- [ 4.0K] 50kb
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+| |-- [ 5.3K] chr21_domain_boundaries.bed
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+| |-- [ 4.4K] chr21_domain_hierachy.tsv
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+| |-- [ 519] chr21_log.txt
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+| |-- [ 7.0K] chr21_sub_compartments.bed
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+| |-- [ 5.4K] chr22_domain_boundaries.bed
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+| |-- [ 4.5K] chr22_domain_hierachy.tsv
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+| |-- [ 519] chr22_log.txt
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+| `-- [ 7.3K] chr22_sub_compartments.bed
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+`-- [ 4.0K] sub_compartments
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+ |-- [ 39K] all_sub_compartments.bed
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+ |-- [ 430K] all_sub_compartments.tsv
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+ |-- [ 47] cor_with_ref.ALL.txt
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+ |-- [ 5.1K] cor_with_ref.pdf
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+ `-- [ 24] cor_with_ref.txt
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```
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The saved .bed files can be view directly through IGV:
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Yuanlong LIU