Bacon

A comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies

For more information, see our Bacon webpage.

Zenodo DOI: 10.5281/zenodo.5607035.

Contents

• Prerequisites
• Example usage
• Trouble shooting

Prerequisites

Python(>=3.4.0) R(>=3.6.2) Homer bedtools

Example usage

1. UV Rate Calculation

Please prepare unfiltered alignment file of all PETs as input, the UV Rate will be printed on the screen.

# Run the commandline
UVRate_calculation.sh align_file.sam /tmpDir

2. PC Calculation

Please prepare at least one loop files (.bedpe format) and place them in a folder, high-quality ChIP-seq/CUT&Run peak file(.bed format).

# Run the commandline
Peak-occupancy.sh /directory_of_loop_folder peak.bed prefix /outDir

3. ES Calculation

Please prepare at least one loop files (.bedpe format) and place them in a folder, uniquely valid PET file (.bedpe format)

# Run the commandline
Enrichment_score.sh  /directory_of_loop_folder ValidPET.bedpe /outDir

4. ACC Calculation

Please prepare at least one loop files (.bedpe format) and place them in a folder, directory of gold standard(true) loop file, and directory of fale loops (you can find in folder /Gold_standard_loops). Here we used dataset_1 as an example:

# Run the commandline
ACC_calculation.sh /directory_of_loop_folder /Gold_standard_loops/true /Gold_standard_loops/false dataset_1 /outDir

5. AR annotation

Please prepare at least one loop files (.bedpe format) and place them in a folder, ccres file of corresponding species (you can find in folder /AR_annotation), tss file of corresponding species (you can find in folder /AR_annotation), active histone mark ChIP-seq peaks (you can find in folder /AR_annotation), inactive histone mark ChIP-seq peaks (you can find in folder /AR_annotation).

# Run the commandline
AR_annotation.sh /directory_of_loop_folder /AR_annotation/hg19_ccres.bed /AR_annotation/GENCODEv19-TSSs.4k.bed /AR_annotation/peaks_k562/active /AR_annotation/peaks_k562/inactive prefix /outDir

6. Simulation

Please choose "simulation_ChIA_PET.R" or "simulation_HiChIP.R" script to perform the simulation.

# Parameters for simulation_ChIA_PET.R
--chr, type="character", List of chromosome names seperated by comma or colon.
--OutDir, type="character", Output directory.
--ChrSizeFile, type="character", The chromosomes size file for reference genome.
--ChIPseqFile, type="character", ChIP-seq file, either alignment (BAM) format, or in bedgraph (4 column) format. Default is NULL.
--TotalRead, type="integer", default=1000000, Total number of reads for the simulated ChIA-PET contacts. Default = 1000000 or 1M.
--BinSize, type="integer", default=5000. Bin size.
--param_a, type="integer", default=100. Parameter a.

# Parameters for simulation_HiChIP.R
--chr, type="character", Comma or colon seperated list of chromosome names for which the simulation would be performed. Default NULL.
--OutDir, type="character", Base Output directory. Mandatory parameter.--ChrSizeFiletype="character", File containing size of chromosomes for reference genome. Mandatory parameter.
--ChIPAlignFile, type="character", ChIP-seq file, either alignment (BAM) format, or in bedgraph (4 column) format. Default is NULL. Mandatory parameter.
--HiCMapFile, type="character", File containing HiC locus pairs and contact counts (7 columns), with respect to the current chromosome.
--TotalRead, type="integer", default=1000000, Total number of reads for the simulated HiChIP contact matrix. Default = 1000000 or 1M.

Trouble shooting

• Stdin error
  Please unzip all the annotation/loop files before running the script.

• Bedtools not found
  Please install bedtools and add the path into system.