/SplicePlot2-1

Visualization toolkit for splicing QTL and circularization QTL

Primary LanguagePython

VISplicing

Visualization toolkit for splicing QTL and circularization QTL

Requirements:

  • 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

Examples

step 1: generate pickle file

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

step 2: make Sashimi plot

python plot.py test_files/chr18:9826168@chr18:9930662-9951252.p pickle settings_file

Sashimi plot

Credits

We would like to thank for the open-sourcing SplicePlot code.