path_FuGePrior_out=path_to_FuGePrior_output_folder

path_to_scripts=path_to_scripts_folder

pegasus_out=path_to_pegasus_output_file

path_to_oncofuse=path_to_oncofuse_tool #path to Oncofuse.jar file

path_to_reference=path_to_fasta_reference_file #This file has to be in fasta format. The folder containing the reference fasta file has to contain also its .fai index. The folder is named REFERENCE

chimerascan_out=chimerascan_output_path #path to chimerscan output files (opportunly modified to perform pergasus run). Each file has to be named "chimeras_sample#.txt" with sample# being the name of the sample specified in data_spec.txt for Pegasus run. 

defuse_out=defuse_output_path #path to defuse output files (opportunly modified to perform pergasus run). Each file has to be named "defuse_sample#.txt" with sampleX being the name of the sample specified in data_spec.txt for Pegasus run.

generic_out=mapsplice_output_path #path to mapsplice output files. Here, differently from what specified for chimeraScan and deFuse files, you have to provide the 'well annotated fusions' file output of MapSplice and not the same files elaborated for Pegasus run. Each file has to be named "generic_sample#.txt" with sample# being the name of the sample specified in data_spec.txt for Pegasus run. 

sample1=sample1_name 
sample2=sample2_name
sampleN=sampleN_name #add a line for each of the sample considered in the analysis. The name of the sample has to be the same used
                     in Pegasus data_spec.txt file

reactive1=reactive1_name
reactive2=reactive2_name
reactiveN=reactiveN_name #add a line for each of the reactive sample considered in the analysis. The name of the sample has          
                          to be the same used in Pegasus data_spec.txt file. 

threshold=numeric_value #This value has to be in the interval [0:1] and represents the Oncofuse/Pegasus score threshold used to filter fusions

unann_string=string_unannotated_genes #List of unannotated genes that you want to filter. Is not necessary to provide the entire gene name. The initial     letters (as AC0, BC0, BC1,...) are sufficient. These names as to be separated by ',' (commas) 

bp_extension=numeric_value #Number of bases used to build the virtual references of the fusion. gene1 and gene2 will be extended of numeric_value bp starting from the detected breakpoints

oncofuse_pathology=string  #This string reports on the origin of the tumor tissue accordingly to Oncofuse run requirements

min_split_overlapping=numeric_value #Minimum overlap between the split reads/consensus region provided by the different chimeric transcript discovery tools and the virtual references built to label the biological mechanism of the fusion






