samples.json

{"seq_mode": "PE", "samples": ["Hi-C_auxin-2days_rep1", "Hi-C_auxin-2days_rep2", "Hi-C_untreated_rep1", "Hi-C_untreated_rep2", "Hi-C_washoff-2days_rep1", "Hi-C_washoff-2days_rep2", "SRR400264_00", "SRR400264_01"], "thread": 20, "bowtie2_index": "/lustre1/chengqiyi_pkuhpc/zhaohn/1.database/db_genomes/genome_fa/genome_ucsc_mm39/genome_ucsc_mm39.fa.bowtie2_index", "bowtie2_params_global": "--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder", "bowtie2_params_local": "--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder", "ligation_site": "AAGCTAGCTT", "sort_ram_per_thread": "", "min_mapq": 10, "bin_sizes": [1000, 2000, 5000, 10000, 20000, 50000, 100000, 200000, 500000, 1000000, 10000000, 50000000, 100000000], "chr_sizes": "program/HiC-Pro_3.1.0/annotation/chrom_mm39.sizes", "digest_bed": "program/HiC-Pro_3.1.0/annotation/HindIII_resfrag_mm39.bed", "restriction_sequence": "AAGCTT", "dangling_sequence": "AGCT"}