PDX Hi-C data processing scripts

Scripts to execute various steps in the PDC Hi-C data analysis.

Scripts were run using PBS job scheduler or in command line.

Each script contains comments about its functionality.

Genomic annotations

• 0a.refgenie.sh - download genomic sequences and assets using refgenie
• 0b.make_annotation_folder.sh - softlink refgeine assets into one folder
• 0c.restriction_sites.sh - create restriction site BED files

Manipulate in silico PDX Hi-C data

• 1.fetchdata.sh - download data from SRA using sratoolkit
• 2a.cutadapt.sh - trim reads to certain length using cutadapt
• 2b.gzipFiles.sh - compress files using gzip
• 3.makePDXs.sh - combine human and mouse reads
• 4a.splitPDXs-xenome.sh - split human and mouse reads using xenome
• 4b.splitPDXs-getHg38Reads.sh - extract human reads using the combined alignment strategy

Processing PDX Hi-C data

• 5a.runHiC-Pro - scripts to run HiC-Pro pipeline

  • config-system.txt - an example of configuration file to install HiC-Pro
  • config_hicpro_hg38.txt - an example of sample-specific configuration file for HiC-Pro
  • 1.run_HiCPro_hg38.sh - a script creating the following files using settings from config_hicpro_hg38.txt
    • 2.HiCPro_step1_PDX.qsub - First step of HiC-Pro pipeline
    • 3.HiCPro_step2_PDX.qsub - Second step of HiC-Pro pipeline
    • inputfiles_PDX.txt - List of samples to process. Only "R1" file is necessary

• 5b.runHiCExplorer - scripts to run HiCExplorer pipeline

  • run_bwamem_R1.sh - aligning R1 reads
  • run_bwamem_R2.sh - aligning R2 reads
  • hicBuildMatrix.sh - run HiCExplorer on the aligned R1 and R2 BAM files

• 5c.runJuicer - scripts to run Juicer pipeline

  • setup_folders.sh - setup folders and softlink raw data for Juicer processing
  • run_juicer.sh - run Juicer on the linked data

• 5d.collectResults - scripts to collect and merge QC metrics from different pipelines

  • 11.hicpro_collectStats.sh - HiC-Pro stats
  • 12.hicpro_mergeStats.sh
  • 21.hicexplorer_collectStats.sh - HiCExplorer stats
  • 22.hicexplorer_mergeStats.sh
  • 31.juicer_collectStats.sh - Juicer stats
  • 32.juicer_mergeStats.sh

Analysis of processed Hi-C data

• 6.convertFileFormats - scripts to convert file formats to .h5

  • hicpro_to_h5.sh - convert HiC-Pro results to .h5 format
  • juicer_to_h5 - scripts for step-wise conversion of Juicer results to .h5 format
    • 1.juicer_to_txt.sh - convert .hic format to text format
    • 2.juicer2hicpro.R - R script to convert text format to matrix. Called by 3.convert_to_hicpro.qsub
    • 3.convert_to_hicpro.sh - convert text format to matrix
    • 4.hicpro_to_h5.sh - convert and KR normalize matrix to .h5 format

• 7.hicPlotDistVsCounts.sh - estimate distance-dependent decay

• 8.TADs.sh - TAD calling using hicFindTADs