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High Resolution and Hierachical Chromosome Modelling

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Bioinformatics, Data Mining, Machine Learning (BDM) Laboratory,

University of Missouri, Columbia MO 65211

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Developer:

             Tuan Trieu
             Department of Computer Science
             University of Missouri, Columbia
             Email: tuantrieu@mail.missouri.edu

Contact:

             Jianlin Cheng, PhD
             Department of Computer Science
             University of Missouri, Columbia
             Email: chengji@missouri.edu

1. Content of folders:

• src: source code in java
• input: sample input data
• output: all HierarchicalModeller experimental output data
• executable: Download latest .jar executable from here : https://github.com/BDM-Lab/Hierarchical3DGenome/releases
• miniMDS: output results and scripts generated for this method

2. Usage

To run the tool, type: java -jar HierarchicalModeller.jar chr_id resolution observed_contact_data normalized_contact_data domain_file output_folder

Example: java -jar HierarchicalModeller.jar 10 5000 input/chr10_5kb.RAWobserved input/chr10_5kb_gm12878_list.txt input/GSE63525_GM12878_primary+replicate_Arrowhead_domainlist_whole.txt output

• Parameters:

  • chr_id: eg. 1, 2, ..
  • resolution: e.g 5000
  • observed_contact_data: observed hi-C contact file, each line contains 3 numbers (separated by a space) of a contact, position_1 position_2 interaction_frequencies (input/chr10_5kb.RAWobserved)(can be downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525)
  • normalized_contact_data: normalized hi-C contact file, each line contains 3 numbers (separated by a space) of a contact, position_1 position_2 interaction_frequencies (input/chr10_5kb_gm12878_list.txt) (can be downloaded and normalized from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525)
  • domain_file: file contains domains identified by Juicer (input/GSE63525_GM12878_primary+replicate_Arrowhead_domainlist_whole.txt) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525)
  • output_folder: output folder

• Typically, the input is several GBs in size and therefore, the program requires a lot of RAM memory to run. We ran our experiment in a server with 120 GB RAM and 80 cores.

4. Disclaimer

The executable software and the source code of is distributed free of charge as it is to any non-commercial users. The authors hold no liabilities to the performance of the program.