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

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

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