Note, only tested on python 3.8.15, pygenometracks 3.6
# create conda environment for pygenometracks
mamba create -n pygenometracks -c bioconda pygenometracks=3.6
# copy SashimiBigWigTrack.py to your pygenometracks library path
cp ./SashimiBigWigTrack.py ./miniconda3/envs/pygenometracks/lib/python3.8/site-packages/pygenometracks/
use sashimi_ingredients.py to prepare for data.
modify plot.sh to plot sashimi plots
run bash plot.sh to plot.
Follow this for pyGenomeTracks installation.
Note, counts files need to be space delimited.
Also, presect rows of counts to include just the intron cluster you want.
You also need to index your vcf file.
also make a list of your sample IDs (one id per line, no header) in a text file.