├── Alighment_ATAC-seq_reads └── ATAC-seq_Alignment.sh ├── HiC_HiChIP_Alignment_and_loop_calling ├── FitHiChIP_configfile_BiasCorrection_CoverageBias_K27-HiChIP.txt ├── FitHiChIP_configfile_BiasCorrection_CoverageBias_K4-HiChIP.txt ├── HiC_HiChIP_Alignment_HiC-pro_config_files.txt ├── Leaf_HiC_HiCcupsloop_calling.sh └── README ├── Identification_of_Differential_ACRs └── Identification_of_Differential_ACRs.sh ├── Identification_of_HighQuality_ACRs ├── 01_calculate_density.sh ├── 02_choose_cutoff.sh ├── 03_prepareTag.sh ├── 04_call_summits.sh └── README ├── Identification_of_Mappable_Regions └── Identification_of_Mappable_Regions.sh ├── README.md └── STARRseq_analysis_scripts ├── bidirectional_analysis ├── betabinomial.pl └── estimate_bidirectional_ACRs.R ├── read_mapping_pipeline └── map_ATAC_Starr_seq_INPUT_example.sh └── regulatory_activity_analysis └── estimate_regulatory_activity.R /Alighment_ATAC-seq_reads/ATAC-seq_Alignment.sh: 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