These script files use the metadata files in the compressed folder named githup_data.tar.gz deposited in the GEO repository (GSE145639) to regenerate the manuscript plots. To run each python or R script file, the script file takes two input arguments. The first input argument is the full path of the folder of the metadata mentioned above, for example: /home/user/githup_data. The second argument is the full path of the folder where to save the file of the output results, for example /home/usrer/Results. All the script files mandatorily need two arguments, but some of the python script files will save the output files in the same input directory.
These tools/packages should be installed and defined in the system path:
- Python v. 2.7
- samtools
- bedtools
- subread
- deeptools v. 3.2.1
- R v. 3.5.0