|
|
@@ -146,7 +146,7 @@ CALDER(contact_file_dump=contact_file_dump,
|
|
|
bin_size=10E3,
|
|
|
genome='hg19',
|
|
|
save_dir=save_dir,
|
|
|
- save_intermediate_data=FALSE,
|
|
|
+ save_intermediate_data=TRUE,
|
|
|
n_cores=2,
|
|
|
sub_domains=TRUE)
|
|
|
```
|
|
|
@@ -253,42 +253,51 @@ CALDER(contact_file_dump=contact_file_dump,
|
|
|
## Output Structure
|
|
|
The output of the workflow is stored in the folder specified by `--save_dir` ("results" by default) and will look like this:
|
|
|
```
|
|
|
-CALDER_dev_output/
|
|
|
-|-- [ 37] intermediate_data
|
|
|
-| `-- [ 56] sub_compartments
|
|
|
-| |-- [ 4.0K] 100kb
|
|
|
-| | |-- [ 2.6K] chr21_domain_boundaries.bed
|
|
|
-| | |-- [ 2.1K] chr21_domain_hierachy.tsv
|
|
|
-| | |-- [ 518] chr21_log.txt
|
|
|
-| | |-- [ 3.4K] chr21_sub_compartments.bed
|
|
|
-| | |-- [ 2.7K] chr22_domain_boundaries.bed
|
|
|
-| | |-- [ 2.2K] chr22_domain_hierachy.tsv
|
|
|
-| | |-- [ 517] chr22_log.txt
|
|
|
-| | `-- [ 3.5K] chr22_sub_compartments.bed
|
|
|
-| |-- [ 4.0K] 10kb
|
|
|
-| | |-- [ 13K] chr21_domain_boundaries.bed
|
|
|
-| | |-- [ 11K] chr21_domain_hierachy.tsv
|
|
|
-| | |-- [ 494] chr21_log.txt
|
|
|
-| | |-- [ 18K] chr21_sub_compartments.bed
|
|
|
-| | |-- [ 15K] chr22_domain_boundaries.bed
|
|
|
-| | |-- [ 13K] chr22_domain_hierachy.tsv
|
|
|
-| | |-- [ 494] chr22_log.txt
|
|
|
-| | `-- [ 21K] chr22_sub_compartments.bed
|
|
|
-| `-- [ 4.0K] 50kb
|
|
|
-| |-- [ 5.3K] chr21_domain_boundaries.bed
|
|
|
-| |-- [ 4.4K] chr21_domain_hierachy.tsv
|
|
|
-| |-- [ 519] chr21_log.txt
|
|
|
-| |-- [ 7.0K] chr21_sub_compartments.bed
|
|
|
-| |-- [ 5.4K] chr22_domain_boundaries.bed
|
|
|
-| |-- [ 4.5K] chr22_domain_hierachy.tsv
|
|
|
-| |-- [ 519] chr22_log.txt
|
|
|
-| `-- [ 7.3K] chr22_sub_compartments.bed
|
|
|
-`-- [ 4.0K] sub_compartments
|
|
|
- |-- [ 39K] all_sub_compartments.bed
|
|
|
- |-- [ 430K] all_sub_compartments.tsv
|
|
|
- |-- [ 47] cor_with_ref.ALL.txt
|
|
|
- |-- [ 5.1K] cor_with_ref.pdf
|
|
|
- `-- [ 24] cor_with_ref.txt
|
|
|
+save_dir/
|
|
|
+|-- intermediate_data
|
|
|
+| |-- sub_compartments
|
|
|
+| | |-- 100kb
|
|
|
+| | | |-- chr21_domain_boundaries.bed
|
|
|
+| | | |-- chr21_domain_hierachy.tsv
|
|
|
+| | | |-- chr21_log.txt
|
|
|
+| | | |-- chr21_sub_compartments.bed
|
|
|
+| | | |-- chr22_domain_boundaries.bed
|
|
|
+| | | |-- chr22_domain_hierachy.tsv
|
|
|
+| | | |-- chr22_log.txt
|
|
|
+| | | `-- chr22_sub_compartments.bed
|
|
|
+| | |-- 10kb
|
|
|
+| | | |-- chr21_domain_boundaries.bed
|
|
|
+| | | |-- chr21_domain_hierachy.tsv
|
|
|
+| | | |-- chr21_intermediate_data.Rds
|
|
|
+| | | |-- chr21_log.txt
|
|
|
+| | | |-- chr21_sub_compartments.bed
|
|
|
+| | | |-- chr22_domain_boundaries.bed
|
|
|
+| | | |-- chr22_domain_hierachy.tsv
|
|
|
+| | | |-- chr22_intermediate_data.Rds
|
|
|
+| | | |-- chr22_log.txt
|
|
|
+| | | `-- chr22_sub_compartments.bed
|
|
|
+| | `-- 50kb
|
|
|
+| | |-- chr21_domain_boundaries.bed
|
|
|
+| | |-- chr21_domain_hierachy.tsv
|
|
|
+| | |-- chr21_log.txt
|
|
|
+| | |-- chr21_sub_compartments.bed
|
|
|
+| | |-- chr22_domain_boundaries.bed
|
|
|
+| | |-- chr22_domain_hierachy.tsv
|
|
|
+| | |-- chr22_log.txt
|
|
|
+| | `-- chr22_sub_compartments.bed
|
|
|
+| `-- sub_domains
|
|
|
+| |-- chr21_nested_boundaries.bed
|
|
|
+| |-- chr21_sub_domains_log.txt
|
|
|
+| |-- chr22_nested_boundaries.bed
|
|
|
+| `-- chr22_sub_domains_log.txt
|
|
|
+|-- sub_compartments ## final sub-compartments
|
|
|
+| |-- all_sub_compartments.bed
|
|
|
+| |-- all_sub_compartments.tsv
|
|
|
+| |-- cor_with_ref.ALL.txt
|
|
|
+| |-- cor_with_ref.pdf
|
|
|
+| `-- cor_with_ref.txt
|
|
|
+`-- sub_domains ## all nested boundaries
|
|
|
+ `-- all_nested_boundaries.bed
|
|
|
```
|
|
|
|
|
|
The saved .bed files can be view directly through IGV:
|
Yuanlong LIU