#==================================== # Sample configuration file for running FitHiChIP #==================================== #***************************** # important parameters #***************************** # File containing the valid pairs from HiCPro pipeline # Can be either a text file, or a gzipped text file ValidPairs=/home/ubuntu/HiChIP_loop_test/data/CTCF-DS.hicpro.valid.pairs.gz # File containing the bin intervals (according to a specified bin size) # which is an output of HiC-pro pipeline # If not provided, this is computed from the parameter 1 Interval= # File storing the contact matrix (output of HiC-pro pipeline) # should be accompanied with the parameter 2 # if not specified, computed from the parameter 1 Matrix= # Pre-computed locus pair file # of the format: # chr1 start1 end1 chr2 start2 end2 contactcounts Bed= # File containing reference ChIP-seq / HiChIP peaks (in .bed format) # mandatory parameter PeakFile=/home/ubuntu/Chip_Peaks/GM12878_CTCF_peaks.bed # Output base directory under which all results will be stored OutDir=/home/ubuntu/HiChIP_loop_test/fithichip_test/fithichip_test_2.5kb #Interaction type - 1: peak to peak 2: peak to non peak 3: peak to all (default) 4: all to all 5: everything from 1 to 4. IntType=1 # Size of the bins [default = 5000], in bases, for detecting the interactions. BINSIZE=2500 # Lower distance threshold of interaction between two segments # (default = 20000 or 20 Kb) LowDistThr=20000 # Upper distance threshold of interaction between two segments # (default = 2000000 or 2 Mb) UppDistThr=2000000 # Applicable only for peak to all output interactions - values: 0 / 1 # if 1, uses only peak to peak loops for background modeling - corresponds to FitHiChIP(S) # if 0, uses both peak to peak and peak to nonpeak loops for background modeling - corresponds to FitHiChIP(L) UseP2PBackgrnd=0 # parameter signifying the type of bias vector - values: 1 / 2 # 1: coverage bias regression 2: ICE bias regression BiasType=1 # following parameter, if 1, means that merge filtering (corresponding to either FitHiChIP(L+M) or FitHiChIP(S+M)) # depending on the background model, would be employed. Otherwise (if 0), no merge filtering is employed. Default: 1 MergeInt=1 # FDR (q-value) threshold for loop significance QVALUE=0.01 # File containing chromomosome size values corresponding to the reference genome. ChrSizeFile=/home/ubuntu/HiChIP_loop_test/data/CTCF-DS.genome # prefix string of all the output files (Default = 'FitHiChIP'). PREFIX=CTCF.DS.2.5kb # Binary variable 1/0: if 1, overwrites any existing output file. otherwise (0), does not overwrite any output file. OverWrite=1