Validation CGRs

The Validation CGRs module allows users to verify the completeness and accuracy of the assembled CGRs.

“Module3”

Inputs

The input files for this module must include the following:

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

  2. A normal Hi-C sample in mcool or cool format.

  3. A assembled CGRs file, which contains assembled CGRs events, is formatted as follows:

haed K562_chr18_assembly_result.txt
num chrom   start   end     node    orient
1   chr18   150000  450000  A       +
1   chr18   21900000        23700000        F       +
1   chr18   8100000 10850000        E       +
1   chr18   1650000 3450000 C       -
2   chr18   450000  800000  B       -
2   chr18   3450000 3850000 G       +
3   chr18   7450000 7700000 D       -
3   chr18   25900000        26500000        H       +

Guideline

Step 1: Load Tumor and Control Samples

Click Tumor Sample to select a tumor Hi-C file, then click Control Sample to select a normal Hi-C file. Click Load to import both files.

Step 2: Select Resolution

Once both Hi-C files are loaded, use the Resolution dropdown menu to select the desired resolution.

Step 3: Load Assembled CGRs File

Click Assembly CGRs File to select a file containing assembled CGRs results.

Step 4: Validate CGRs with Simulated Hi-C Map

Click Validation to generate a simulated Hi-C map. The results will display on the right, allowing you to visually compare abnormal interaction regions in the original and simulated Hi-C maps for validation.

Step 5: Reset Visualization for New Validation

Click Reset Visualization to load a new assembled CGRs file for validation.

To reinitialize the module, click Reset.

Output

“Module4”