PASSion V1.2.0 Manual

For one library

Usage: passion.pl Arguments Options
Arguments:
    -s/--insert_size    	insert size                                                 
    -r/--read1          	read1                                                       
    -f/--read2          	read2                                                       
    -R/--ref            	the reference sequence                                      
    -I/--refindex       	the reference index using SMALT                             
Options:
    -c/--cutoff         	cutoff=(number of support reads)/(coverage of higher expressed flanking exon) [default 0.1]
    -d/--divide2files   	divide bed file according to split sites [default F]        
    -x/--exonisland_file	user defined exon islands file in GFF or GTF format (the 1st, 4th, and 5th fields 
                                are the coordinates in the genome instead of relative location in a gene) [default F]
    -S/--max_SNP        	max number of SNP allowed [default 2]                       
    -M/--max_intron_index	maximum intron index [default 7]
                                [1]=100; [2]=400; [3]=1600; [4]=6400; [5]=25600; [6]=102400; [7]=409600;
                                [8]=1638400; [9]=6553600; [10]=26214400; [11]=104857600; [12]=419430400;
    -m/--min_tron       	minimum intron size [default 20]                            
    -o/--output_folder  	output folder [default ./passion_output]                    
    -e/--sequence_error 	sequence error rate [default 0.05]                          
    -T/--thread         	number of thread [default 1]                                
    -w/--window_size    	window size [default 5000000]                               
    -h/--help           	help                                                        
    -v/--version        	version   

Detect differential splicing pattern in multiple samples:

Usage: passion_diff.pl Arguments Options
Arguments:
    -f/--configurefile  	configuration file format: passion_output_path tag (separate by \t)
Options:
    -c/--cutoff         	cutoff=(number of support reads)/(coverage of higher expressed flanking exon) [default 0.1]
    -d/--dividebysite   	divide bed file according to split sites [default F]        
    -o/--outputfolder   	output folder [default ./passion_diff_output]               
    -h/--help           	help                                                        
    -v/--version        	version  

One example of user-defined exon region in GFF format

track name=regulatory description="TeleGene(tm) Regulatory Regions"
#hello
chr17	TeleGene	enhancer	1000000	1001000	500	+	.	touch1
chr17	TeleGene	promoter	1010000	1010100	900	+	.	touch1
chr17	TeleGene	promoter	1020000	3020000	800	-	.	touch2

One example of multiple sample configure file

./s8_passion_output	s8
./s1_passion_output	s1
./s2_passion_output	s2

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