- numpy
- scipy
- matplotlib
- h5py
- pp (Parallel Processing)
- Biopython
- pymongo
- mirnylib (https://bitbucket.org/mirnylab/mirnylib)
- networkx
- bowtie2
- 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.