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@@ -234,57 +234,57 @@ CALDER(contact_file_dump=contact_file_dump,
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The output of the workflow is stored in the folder specified by `save_dir` and will look like this:
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```
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save_dir/
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-|-- intermediate_data
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-| |-- sub_compartments
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-| | |-- 100kb
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-| | | |-- chr21_domain_boundaries.bed
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-| | | |-- chr21_domain_hierachy.tsv
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-| | | |-- chr21_log.txt
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-| | | |-- chr21_sub_compartments.bed
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-| | | |-- chr22_domain_boundaries.bed
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-| | | |-- chr22_domain_hierachy.tsv
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-| | | |-- chr22_log.txt
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-| | | `-- chr22_sub_compartments.bed
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-| | |-- 10kb
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-| | | |-- chr21_domain_boundaries.bed
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-| | | |-- chr21_domain_hierachy.tsv
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-| | | |-- chr21_intermediate_data.Rds
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-| | | |-- chr21_log.txt
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-| | | |-- chr21_sub_compartments.bed
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-| | | |-- chr22_domain_boundaries.bed
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-| | | |-- chr22_domain_hierachy.tsv
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-| | | |-- chr22_intermediate_data.Rds
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-| | | |-- chr22_log.txt
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-| | | `-- chr22_sub_compartments.bed
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-| | `-- 50kb
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-| | |-- chr21_domain_boundaries.bed
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-| | |-- chr21_domain_hierachy.tsv
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-| | |-- chr21_log.txt
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-| | |-- chr21_sub_compartments.bed
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-| | |-- chr22_domain_boundaries.bed
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-| | |-- chr22_domain_hierachy.tsv
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-| | |-- chr22_log.txt
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-| | `-- chr22_sub_compartments.bed
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-| `-- sub_domains
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-| |-- chr21_nested_boundaries.bed
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-| |-- chr21_sub_domains_log.txt
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-| |-- chr22_nested_boundaries.bed
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-| `-- chr22_sub_domains_log.txt
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-|-- sub_compartments ## final sub-compartments
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-| |-- all_sub_compartments.bed
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-| |-- all_sub_compartments.tsv
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-| |-- cor_with_ref.ALL.txt
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+|-- sub_domains
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+| `-- all_nested_boundaries.bed
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+|-- sub_compartments
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+| |-- cor_with_ref.txt
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| |-- cor_with_ref.pdf
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-| `-- cor_with_ref.txt
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-`-- sub_domains ## all nested boundaries
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- `-- all_nested_boundaries.bed
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+| |-- cor_with_ref.ALL.txt
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+| |-- all_sub_compartments.tsv
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+| `-- all_sub_compartments.bed
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+`-- intermediate_data
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+ |-- sub_domains
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+ | |-- chr22_sub_domains_log.txt
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+ | |-- chr22_nested_boundaries.bed
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+ | |-- chr21_sub_domains_log.txt
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+ | `-- chr21_nested_boundaries.bed
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+ `-- sub_compartments
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+ |-- 50kb
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+ | |-- chr22_sub_compartments.bed
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+ | |-- chr22_log.txt
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+ | |-- chr22_domain_hierachy.tsv
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+ | |-- chr22_domain_boundaries.bed
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+ | |-- chr21_sub_compartments.bed
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+ | |-- chr21_log.txt
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+ | |-- chr21_domain_hierachy.tsv
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+ | `-- chr21_domain_boundaries.bed
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+ |-- 10kb
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+ | |-- chr22_sub_compartments.bed
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+ | |-- chr22_log.txt
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+ | |-- chr22_intermediate_data.Rds
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+ | |-- chr22_domain_hierachy.tsv
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+ | |-- chr22_domain_boundaries.bed
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+ | |-- chr21_sub_compartments.bed
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+ | |-- chr21_log.txt
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+ | |-- chr21_intermediate_data.Rds
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+ | |-- chr21_domain_hierachy.tsv
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+ | `-- chr21_domain_boundaries.bed
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+ `-- 100kb
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+ |-- chr22_sub_compartments.bed
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+ |-- chr22_log.txt
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+ |-- chr22_domain_hierachy.tsv
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+ |-- chr22_domain_boundaries.bed
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+ |-- chr21_sub_compartments.bed
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+ |-- chr21_log.txt
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+ |-- chr21_domain_hierachy.tsv
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+ `-- chr21_domain_boundaries.bed
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```
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### File description:
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-* The sub_compartments folder stores the final compartment information
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-* The sub_domains folder stores the final nested boundaries information
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-* The intermediate_data folder stores information at each of the extended `bin_sizes`
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+* The `sub_domains` folder stores the final nested boundaries information
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+* The `sub_compartments` folder stores the final compartment information
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+* The `intermediate_data` folder stores intermediate information at each of the extended `bin_sizes`
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#### chrxx_domain_hierachy.tsv
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* information of compartment domain and their hierarchical organization. The hierarchical structure is fully represented by `compartment_label`, for example, `B.2.2.2` and `B.2.2.1` are two sub-branches of `B.2.2`. The `pos_end` column specifies all compartment domain borders, except when it is marked as `gap`, which indicates it is the border of a gap chromsome region that has too few contacts and was excluded from the analysis (e.g., due to low mappability, deletion, technique flaw)
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Yuanlong LIU