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
Last modified 11 years ago
Last modified on Dec 29, 2011, 7:05:39 PM