
 This is the test suite for siRNA discovery pipeline.
 You will use the siRNA off-target discovery pipeline to compute 
 an off-targeting potential for a given siRNA and to detect the
 potential off-target transcripts.

 !! You first need to make sure that risearch2.x and RNAplfold
    commands are both executable from terminal.

#####################################################################
 You can run the following commands from the test_suite folder, 
 to compute a genome-wide off-targeting potential with dummy data.

==================
 mkdir gw_test
 cd gw_test
 mkdir RIsearch2_results
 cd RIsearch2_results
 risearch2.x -c ../../genome.fa -o genome.pksuf
 risearch2.x -q ../../sirna.fa -i genome.pksuf -s 1:12/6 -e -10 -l 20
 cd ..
 mkdir accessibility_results
 cd accessibility_results
 ../../../src/run_RNAplfold_and_pack_results.py ../../genome.fa 80 40 +
 ../../../src/run_RNAplfold_and_pack_results.py ../../genome.fa 80 40 -
 cd .. 
 ../../src/pipeline.py -r RIsearch2_results/risearch_siRNAID.out.gz \
    -t ../expression_data.gtf -feature transcript -expmetric RPKM \
    -p accessibility_results/ -q siRNAID -os ../sirna.fa \
    -o sirna_gw_off_targets.txt --offPs -oi onTarget --sort 
 cd ..
==================

 This run should have generated the gw_test/sirna_gw_off_targets.txt file 
 that reports the off-targeting probabilities of potential transcripts and
 off-targeting potential of the siRNA with an ID of siRNAID.

 You can compare this file with gw.results file we provide within the 
 test suite, to see if you have actually generated the right results.

 diff gw_test/sirna_gw_off_targets.txt gw.results

 # !!! WARNING: This might fail if you are not using Vienna package 2.2.5

#####################################################################

 To make a transcriptome_wide prediction with dummy data, you can run the 
 following commands.

==================
 mkdir tw_test
 cd tw_test
 mkdir RIsearch2_results
 cd RIsearch2_results
 risearch2.x -c ../../transcripts.fa -o transcripts.pksuf
 risearch2.x -q ../../sirna.fa -i transcripts.pksuf -s 1:12/6 -e -10 -l 20
 cd ..
 mkdir accessibility_results
 cd accessibility_results/
 ../../../src/run_RNAplfold_and_pack_results.py ../../transcripts.fa 80 40 +
 cd ..
 ../../src/pipeline.py -r RIsearch2_results/risearch_siRNAID.out.gz --less \
    -type tw -t ../expression_data.bed -p accessibility_results/ -q siRNAID \
    -os ../sirna.fa -o sirna_tw_off_targets.txt --offPs \
    -of ../onTarget.fa -oexp 1000
===================

 
 This run should have generated the tw_test/sirna_tw_off_targets.txt file 
 that reports the off-targeting probabilities of potential transcripts and
 off-targeting potential of the siRNA with an ID of siRNAID.

 You can compare this file with tw.results file we provide within the 
 test suite, to see if you have actually generated the right results.

 diff tw_test/sirna_tw_off_targets.txt tw.results

 # !!! WARNING: This might fail if you are not using Vienna package 2.2.5

