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- #######################
- # globe
- #######################
- # HiCSnake 流程所在位置
- HICSNAKE_HOME: /home/zhxd/workspace/20240527_HiC/HicSnake
- # 基因组前缀 ref/$genome.fa
- genome: genome
- # 酶的识别位点
- restriction_sequence: GATC
- #######################
- # resolutions
- #######################
- # 所有分辨率, 最小值为基础分辨率, 其他值应为基础分辨率的整倍
- resolutions:
- - 1000
- - 2000
- - 5000
- - 10000
- - 15000
- - 20000
- - 25000
- - 40000
- - 100000
- - 250000
- - 500000
- - 1000000
- # CALDER2 的分辨率, 10kb~100kb, 可设置多个
- Compartment_resolution:
- - 40000
- # hicFindTADs 的分辨率, 40kb ~ 100kb, 可设置多个
- TAD_resolution:
- - 40000
- # Mustache 的分辨率, 1kb ~ 20kb, 可设置多个
- Loop_resolution:
- - 10000
- Plot_matrix_resolution:
- - 40000
- #######################
- # paramaters
- #######################
- # fastp 过滤
- fastp: "--adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --qualified_quality_phred 20 --length_required 50"
- # 构建矩阵
- hicBuildMatrix: "--minDistance 500 --maxLibraryInsertSize 1500 --inputBufferSize 1000000 --restrictionSequence GATC --danglingSequence GATC"
- # 样本间标准化, 不用改
- hicNormalize: "--normalize smallest"
- # 参考https://github.com/TaoYang-dev/hicrep
- hicrep: "--h 20 --dBPMax 500000"
- # 计算分辨率
- hicres: "--resolutions 1000,2000,5000,10000"
- # 使用 Calder2 检测 subcompartment, -f 指定 feature track, --chr_prefix 指定原染色体前缀,需要统一
- calder: "-g others -f ref/gene_density.bed --chr_prefix Chr"
- #
- hicFindTADs: " --correctForMultipleTesting fdr --thresholdComparisons 0.01 --delta 0.01"
- hicDifferentialTAD: "--pValue 0.05 --mode all --modeReject one"
- hicDetectLoops: "--maxLoopDistance 2000000 --windowSize 10 --peakWidth 6 --pValuePreselection 0.05 --pValue 0.05"
- #mustache: "-pt 0.05 -st 0.88"
- mustache: ""
- #diff_mustache: "-pt 0.05 -pt2 0.05 -st 0.88"
- diff_mustache: ""
- hicPlotDistVsCounts: ""
- stripenn: ""
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