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
