A set of C++ utilities for pre/post-processing Hi-C data for public software (including CscoreTool for A/B compartment, TopDom for TAD, and Fit-Hi-C for significant contacts), for data visualization with the WashU Epigenome Browser, and for quality inspection.
Installation
After download the package, locate the folder using terminal command, and type in: "sh iHiC_install" to compile the C++ codes with g++. Executive files will be save to a sub_folder "bin". Add the "bin" folder to your path or copy the executive files to /usr/bin/ or /usr/local/bin.
Descriptions of usage of the utilities
-
iHiC_BEDPE_Statistics: Calculate statistics of PET alignments from a simplified BEDPE file.
Usage: iHiC_BEDPE_Statistics BEDPE_file MAPQ
Inputs:
BEDPE_file: A simplified version of regular BEDPE file: only columns for “chrom1”, “start1”, “end1”, “chrom2”, “start2”, “end2”, “score”, “strand1”, and “strand 2” are retained.
MAPQ: Minimal mapping quality score used to filter out PETs mapped to multiple positions. 10 recommended.
Outputs: screen -
iHiC_PETOrientations_Stat: Calculate % of PETs in different combinations of orientations as a function of genomic distance.
Usage: iHiC_PETOrientations_Stat BEDPE_file MAPQ
BEDPE_file: A simplified version of regular BEDPE file: only columns for “chrom1”, “start1”, “end1”, “chrom2”, “start2”, “end2”, “score”, “strand1”, and “strand 2” are retained.
MAPQ: Minimal mapping quality score used to filter out PETs mapped to multiple positions. 10 recommended.
Outputs: screen -
iHiC_ContactFreq_Distance: Calculate contact probability as a function genomic distance.
Usage: iHiC_ContactFreq_Distance BEDPE_file MAPQ
BEDPE_file: A simplified version of regular BEDPE file: only columns for “chrom1”, “start1”, “end1”, “chrom2”, “start2”, “end2”, “score”, “strand1”, and “strand 2” are retained.
MAPQ: Minimal mapping quality score used to filter out PETs mapped to multiple positions. 10 recommended.
Outputs: screen
Note: It is recommended to redirect the ouputs into a local file with the ">" symbol: iHiC_ContactFreq_Distance BEDPE_file MAPQ > local_file_name -
iHiC_BEDPE2III: Generate an intra-chromosomal interaction index (III) file that records the numbers of PETs for interacting genomic bins from the same chromosomes.
Usage: iHiC_BEDPE2III BEDPE_file Bin_size Minimal_Distance Maximal_Distance MAPQ Output_file_name
Inputs:
BEDPE_file: A simplified version of regular BEDPE file: only columns for “chrom1”, “start1”, “end1”, “chrom2”, “start2”, “end2”, “score”, “strand1”, and “strand 2” are retained.
Bin_size: Used to partition the genome into bins of equal size.
Minimal_Distance: Minimal distance between two PET ends considered for downstream analysis. Should be no less than Bin_size.
Maximal_Distance: Maximal distance between two PET ends considered for downstream analysis. Simply set to 2000,0000,000 bps to include all interacting PETs longer than the Minimal_Distance. However, considering that majority of the significant contacts are less than 2,000,000 bps, one may want to set Maximal_Distance to this number to save computational time for later analysis.
MAPQ: Minimal mapping quality score used to filter out PETs mapped to multiple positions. 10 recommended.
Output_file_name: File name for the III file.
Outputs: Format for left to right columns: chromosome, genomic position of bin1, genomic position of bin2, number of PETs linking the two bins.
Note: Only uniquely mapped PETs are considered. For multiple PETs mapped to the same position, only one copy is retained. -
iHiC_III2WashU: Convert an III file into “longrange” format accepted by the WashU Epigenome Browser.
Usage: iHiC_III2WashU III_file Bin_size Output_file_name
Inputs:
III_file: An intra-chromosomal interaction index (III) file that records the numbers of PETs for interacting genomic bins from the same chromosomes. Output from iHiC_BEDPE2III.
Bin_size: Size of genomic bin.
Output_file_name: File name for the "longrange" file.
Outputs: A "longrange" format by WashU Epigenome Browser. -
iHiC_BEDPE2HiCSummary: Convert a BEDPE file into “HiCsummary” format accepted by CscoreTool.
Usage:iHiC_BEDPE2HiCSummary BEDPE Output_file_name
Inputs:
BEDPE_file: A simplified version of regular BEDPE file: only columns for “chrom1”, “start1”, “end1”, “chrom2”, “start2”, “end2”, “score”, “strand1”, and “strand 2” are retained.
Output_file_name: File name for the "HiCsummary" file.
Outputs:In "HiCsummary" format -
iHiC_Cscore_Adj: Flip the sign of C-score chromosome-by- chromosome to ensure genomic regions with positive scores correspond to A compartment status.
Usage: iHiC_Cscore_Adj Cscore_file CpG_annotation_file
Inputs:
Cscore_file: output file from Cscore_Tool with name ending with '_cscore.bedgraph'
CpG_annotation_file: CpG annotation downloaded from UCSC. Only the 4-5 columns corresponding to chr, start and end are used by the program.
Outputs: A "bedgraph" format with file name ending with "adj" -
iHiC_III2MTX4TopDom: Convert an III file into interaction matrices accepted by TopDom.
Usage:iHiC_III2MTX4TopDom III_file Bin_size Chr_lenth_file Output_Prefix
Inputs:
III_file: An intra-chromosomal interaction index (III) file that records the numbers of PETs for interacting genomic bins from the same chromosomes. Output from iHiC_BEDPE2III.
Bin_size: Size of genomic bin.
Chr_lenth_file: In a two column format: chr and length
Output_Prefix: "chr#.mtx4topdom" will be appended to the Output_Prefix to denote the file for chr#.
Outputs: In the format of n X (n+3) matrix format, accepted by TopDom as input, with first three columns for bin.chr, bin.start, and bin.end, and the next n columns for # of PETs linked to other bins. -
iHiC_TADBoundary_TopDom: Extract TAD boundaries from TopDom predictions.
Usage:iHiC_TADBoundary_TopDom TopDom_binSignal_file Pvalue_threshold Output_file_name
Inputs:
TopDom_binSignal_file: Output file from TopDom with name ending with '.binSignal'.
Pvalue_threshold: Pvalue used to filter bins corresponding to TAD boundaries.
Output_file_name: File name for the file of TAD boundaries.
Outputs:In bedgraph format. -
iHiC_III2FitHiCInputs: Convert an III file into interaction matrices accepted by Fit-Hi-C.
Usage: iHiC_III2FitHiCInputs III Output_prefix Chr_length_file Bin_size Minimal_Distance Maximal_Distance
Inputs:
III_file: An intra-chromosomal interaction index (III) file that records the numbers of PETs for interacting genomic bins from the same chromosomes. Output from iHiC_BEDPE2III.
Output_Prefix: "chr#.frag" and "chr#.cnts" will be appended to the Output_Prefix to denote the files for chr#.
Chr_lenth_file: In a two column format: chr and length
Bin_size: Size of genomic bin.
Minimal_Distance: Minimal distance between two PET ends considered.
Maximal_Distance: Maximal distance between two PET ends considered
Outputs: "chr#.frag" and "chr#.cnts" for "fragments file" and "interactions file" accepted by Fit-Hi-C -
iHiC_FitHiC2WashU: Convert the significant contacts predicted by Fit-Hi-C into a “longrange” format accepted by the WashU Epigenome Browser.
Usage: iHiC_FitHiC2WashU FitHiC_prediction Bin_size Q-value
Inputs:
FitHiC_prediction: Output file Fit-Hi-C with name ending with '.significances.txt'.
Bin_szie: Bin size used for generating inputs for Fit-Hi-C by iHiC_III2FitHiCInputs
Q-value: Q-value to retain significant contacts.
Outputs: Output file will be ending with "longrange" accepted by WashU Epigenome Browser for data visualization. -
TopDom_wrapper.R: A Rscript wrapper to runn TopDom.
Usage: Rscript TopDom_wrapper.R Path_to_TopDom_v0.0.2.R ".mtx4topdom"_file.
The file ".mtx4topdom" are outputs from "iHiC_III2MTX4TopDom".
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