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@@ -115,8 +115,8 @@ CALDER_sub_domains(intermediate_data_file,
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| **contact_tab_straw** |
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| **ref_genome** | One of 'hg19', 'hg38', 'mm9', 'mm10', or 'others' by default.
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-| **select** | Selection of best PC for downstream analysis [Must be after cis or trans step]
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-| **analyze** | Perform differential analysis on selected PC's [Must be after select step]
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+| **annotation_track** | A table in data.frame or data.table format
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+| **contact_file_hic** | Path to the hic file
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| **subcomp** | Optional: Assigning sub-compartments based on PC magnitude values using HMM segmentation
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| **fithic** | Run [Fit-Hi-C](https://github.com/ay-lab/fithic) to identify loops before running dloop (Optional but recommended)
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| **dloop** | Find differential loops anchored in at least one of the differential compartments across the samples (Optional but recommended)
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Yuanlong LIU