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@@ -229,29 +229,9 @@ CALDER(contact_file_dump=contact_file_dump,
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| **sub_domains** | logical, whether to compute nested sub-domains
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-### Output:
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-
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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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-
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-#### chrxx_sub_compartments.bed
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-* 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)
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-
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-#### chrxx_domain_boundaries.bed
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-* a .bed file containing the chromatin domains boundaries, that can be visualized in IGV
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-
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-#### chrxx_nested_boundaries.bed
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-* a .bed file containing the nested sub-domain boundaries, that can be visualized in IGV
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-
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-#### chrxx_intermediate_data.Rds
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-* an Rds file storing the intermediate_data that can be used to compute nested sub-domains (if CALDER is run in two seperated steps)
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-
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-#### chrxx_log.txt, chrxx_sub_domains_log.txt
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-* log file storing the status and running time of each step
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-
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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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+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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@@ -300,6 +280,28 @@ save_dir/
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`-- all_nested_boundaries.bed
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```
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+### File description:
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+
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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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+
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+#### chrxx_sub_compartments.bed
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+* 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)
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+
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+#### chrxx_domain_boundaries.bed
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+* a .bed file containing the chromatin domains boundaries, that can be visualized in IGV
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+
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+#### chrxx_nested_boundaries.bed
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+* a .bed file containing the nested sub-domain boundaries, that can be visualized in IGV
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+
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+#### chrxx_intermediate_data.Rds
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+* an Rds file storing the intermediate_data that can be used to compute nested sub-domains (if CALDER is run in two seperated steps)
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+
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+#### chrxx_log.txt, chrxx_sub_domains_log.txt
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+* log file storing the status and running time of each step
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+
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+
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+
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The saved .bed files can be view directly through IGV:
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Yuanlong LIU