Visualization toolkit for splicing QTL and circularization QTL
- Python 2.7
- pandas package
- pysam package
- matplotlib, scipy, and numpy
- samtools must be installed and in your $PATH
- tabix must be installed and in your $PATH
python initialize_data.py chr18:9826168 chr18:9930662-9951252 --vcf test_files/SNP.chr18_9826168.vcf.gz --gtf test_files/HG19.gtf --mf test_files/map_file.txt --circ test_files/chr18_9931806_9950565.circRNA.rawcount.txt --output test_files
python plot.py test_files/chr18:9826168@chr18:9930662-9951252.p pickle settings_file
We would like to thank for the open-sourcing SplicePlot code.