Dependencies

Python packages

Make sure you have read/write/execute permission on the main folder and all its subfolders.
Run main.py
Choose output folder
Load a fasta genome
Build bowtie index (bowtie path must be specified in the advanced options or a bowtie folder must be in the main folder)
Load fastq paired-end read files
Load restriction enzyme (or manually type in the site sequence)
Check advanced parameters and tweak if needed
Align and wait for ready for computation terminal output (this may take a while)
Click on Pyramid to proceed to the visualizer (visualizer may also be directly summoned by running main_window.py)
Load data and browse to the inside of a folder named analysis within the output folder
Build pyramid (this may take a while) and load it
Visualize using options as needed

When building a pyramid, the sparsity filter will remove bins whose total contact count is too low.
Saturation threshold can be either absolute (fixed number), relative (percentile, append % at the end) or auto-adjusted depending on the needed rendering.
Matrices can be manually loaded "raw" (from a text file) and binned, but no genome information will be displayed.
"Kb binning" will regroup bins such that the total length of each bin is closest to 10kb.
The norm called sparsity is an alias for fragment-wise order 1 normalization.