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