Reconstruct Hi-C Map

The Reconstruct Hi-C Map module generate a reconstructed Hi-C map based on the identified CGR event.

“Module4”

Inputs

The input files for this module need to provide the following:

  1. A tumor Hi-C sample in mcool or cool format.

  2. A CGR file, which contains a CGR event, is formatted as follows:

haed K562_chr18_CGR.txt
chrom       start   end     node    orient
chr18       150000  450000  A       +
chr18       21900000        23650000        B       +
chr18       8100000 10850000        F       +
chr18       1650000 3450000 E       -

Guideline

Step 1: Load Tumor Sample

Click Tumor Sample to select a tumor Hi-C file, and then click Load to import the file.

Step 2: Select Resolution

Once the Hi-C file is loaded, use the Resolution dropdown menu to choose the desired resolution.

Step 3: Load CGR Event File

Click CGR File to select a file containing a CGR event.

Step 4: CNV normalization (To better visualization)

Click CNV Normalization. In the popup window, select the reference genome and enzyme for the Hi-C sample, and adjust nproc based on available computational resources.

Parameter Descriptions (for detailed information, see NeoLoopFinder):

  • Ref Genome: The reference genome used for mapping the Hi-C data. Supported genomes include: hg38, hg19, mm10, and mm9.

  • Enzyme: The restriction enzyme used in the Hi-C experiment. Supported enzymes include: HindIII, MboI, DpnII, BglII, Arima, and uniform. Use uniform if the genome was digested with a sequence-independent or uniformly cutting enzyme.

  • nproc: The number of processing threads to use, specified as an integer (e.g., 10).

“CNV_normalization_parameter_setting”

Step 5: Reconstruct Hi-C Map

Click Reconstruct to generate a reconstructed Hi-C map.

Step 6: Export Results

Click Export Result to export the reconstructed Hi-C contact matrix.

To reinitialize the module, click Reset.

Output

“Module4”