to run the pipeline: 1)compress all of your fastq files with gzip and place them in one folder 2)fill out a settings file, pay attention to the output location, or you risk overwriting previous runs 3)from the mod_seq folder run: python mod_seq_main.py my_experiment.settings.json
optional parameters (add after settings file): --threads : max number of parrallel processes to use. Default is 8.
Python dependencies (install with pip): simplejson bokeh (optional, but very helpful) statsmodels matplotlib numpy scipy
This package requires installation of the ShapeMapper package from Kevin Weeks' lab. Download ShapeMapper 2 from http://www.chem.unc.edu/rna/software.html compile it, and add it to your PATH.
skewer is required: https://github.com/relipmoc/skewer
seqtk is required: https://github.com/lh3/seqtk
pigz is required: https://zlib.net/pigz/
STAR is required, add to PATH: https://github.com/alexdobin/STAR
the bokeh interactive plotting package is optionally required: http://bokeh.pydata.org/en/latest/docs/user_guide/quickstart.html#userguide-quickstart
explanation of settings files: since I can't figure out how to add comments to the settings files, please read settings.explanation.txt