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@@ -303,15 +303,15 @@ save_dir/
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| **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)
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| **chrxx_domain_boundaries.bed** | a .bed file containing the chromatin domains boundaries, that can be visualized in IGV
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| **chrxx_nested_boundaries.bed** | a .bed file containing the nested sub-domain boundaries, that can be visualized in IGV
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-| **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)
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-| **chrxx_log.txt, chrxx_sub_domains_log.txt** | log file storing the status and running time of each step
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+| **chrxx_intermediate_data.Rds** | an Rds file storing the intermediate_data that can be used to compute nested sub-domains
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+| **chrxx_log.txt, chrxx_sub_domains_log.txt** | log files storing the status and running time of each step
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-The saved .bed files can be view directly through IGV:
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+All .bed files can be view directly through IGV:
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-### Runnig time:
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+# Runnig time:
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For the computational requirement, running CALDER on the GM12878 Hi-C dataset at bin size of 40kb took **36 minutes** to derive the chromatin domains and their hierarchy for all chromosomes (i.e., CALDER Step1 and Step2); **13 minutes** to derive the nested sub-domains (i.e., CALDER Step3). At the bin size of 10kb, it took **1 h 44 minutes and 55 minutes** correspondingly (server information: 40 cores, 64GB Ram, Intel(R) Xeon(R) Silver 4210 CPU @ 2.20GHz). The evaluation was done using a single core although CALDER can be run in a parallel manner.
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# Citation
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Yuanlong LIU