Requirements:

Jupyter notebook - recommended to install by downloading Anaconda

• https://jupyter.org/install

pysam module - if not installed type conda install -c bioconda pysam in terminal

• https://anaconda.org/bioconda/pysam

To download notebook from github to local computer:

• Easy method:

1. Right-click and save this file: https://raw.githubusercontent.com/dgranas/pseudo-seq/master/5-2-19_analysis.ipynb
2. You will also need the known rRNA sites file: https://raw.githubusercontent.com/dgranas/pseudo-seq/master/Carlile_known_human_SuppT7_updated.csv
3. Use the terminal to go to the directory containing these files and type jupyter notebook

• Alternate method using git clone:

1. open terminal and go to directory where you want to put the folder
2. type git clone https://github.com/dgranas/pseudo-seq.git
3. Run jupyter notebook in this directory by typing jupyter notebook in the terminal