This repository contains all code used to process BTV shape data. There are two scripts:
- map_raw_data.sh - this contains the code to map the fastq data to the reference genome and produce map files
- shape_map_figures.ipynb - this is an interactive python notebook that contains the code to process the map files and produce the figures
Additionally tsv files prodiced by delta shape are located in the data folder. These files are used as input for the shape_map_figures.ipynb script.