|
@@ -282,13 +282,13 @@ save_dir/
|
|
|
|
|
|
### File description:
|
|
|
|
|
|
-* The `sub_domains` folder stores the final nested boundaries information
|
|
|
+* The `sub_domains` folder stores the final nested boundaries
|
|
|
* The `sub_compartments` folder stores the optimal compartment information, including files:
|
|
|
|
|
|
| Name | Description |
|
|
|
| --------------------- | ----------------------- |
|
|
|
-| **all_sub_compartments.bed** | a .bed file containing the optimal sub-compartment information for all `chrs`, that can be visualized in IGV. Different colors were used to distinguish compartments (at the resolution of 8 sub-compartments)
|
|
|
-| **all_sub_compartments.tsv** | optimal compartment information stored in tabular text format. Each row represents one 10kb region
|
|
|
+| **all_sub_compartments.bed** | a .bed file containing the optimal compartments for all `chrs`, that can be visualized in IGV. Different colors were used to distinguish compartments (at the resolution of 8 sub-compartments)
|
|
|
+| **all_sub_compartments.tsv** | optimal compartments stored in tabular text format. Each row represents one 10kb region
|
|
|
| **all_sub_compartments.tsv** | optimal compartment information stored in tabular text format. Each row represents one 10kb region
|
|
|
| **cor_with_ref.ALL.txt** | correlation of compartment rank with the reference compartment rank for each of `bin_sizes`, and the optimimal `bin_size` that is finally selected
|
|
|
| **cor_with_ref.pdf** | correlation of compartment rank with the reference compartment rank using the optimimal `bin_size`
|
|
@@ -301,7 +301,7 @@ save_dir/
|
|
|
| Name | Description |
|
|
|
| --------------------- | ----------------------- |
|
|
|
| **chrxx_domain_hierachy.tsv** | 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)
|
|
|
-| **chrxx_sub_compartments.bed** | a .bed file containing the sub-compartment information, that can be visualized in IGV. Different colors were used to distinguish compartments (at the resolution of 8 sub-compartments)
|
|
|
+| **chrxx_sub_compartments.bed** | a .bed file containing the compartment information, that can be visualized in IGV. Different colors were used to distinguish compartments (at the resolution of 8 sub-compartments)
|
|
|
| **chrxx_domain_boundaries.bed** | a .bed file containing the chromatin domains boundaries, that can be visualized in IGV
|
|
|
| **chrxx_nested_boundaries.bed** | a .bed file containing the nested sub-domain boundaries, that can be visualized in IGV
|
|
|
| **chrxx_intermediate_data.Rds** | an Rds file storing the intermediate_data that can be used to compute nested sub-domains (if CALDER is run in two seperated steps)
|