Requirements:
Jupyter notebook - recommended to install by downloading Anaconda
pysam module - if not installed type conda install -c bioconda pysam
in terminal
To download notebook from github to local computer:
- Easy method:
- Right-click and save this file: https://raw.githubusercontent.com/dgranas/pseudo-seq/master/5-2-19_analysis.ipynb
- You will also need the known rRNA sites file: https://raw.githubusercontent.com/dgranas/pseudo-seq/master/Carlile_known_human_SuppT7_updated.csv
- Use the terminal to go to the directory containing these files and type
jupyter notebook
- Alternate method using git clone:
- open terminal and go to directory where you want to put the folder
- type
git clone https://github.com/dgranas/pseudo-seq.git
- Run jupyter notebook in this directory by typing
jupyter notebook
in the terminal