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Dependencies

Python packages

Other software

  • bowtie2

How to use

  • 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

Advanced

Visualizer options

  • 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.

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