PIWI_PIPELINE.sh is a master script that generates PBS job scripts for trimming, mapping + feature assignment to all GTFs. It should generate these for all *.fastq$ files in ${dir}raw_data/. Once the trimming scripts are done, then run the bowtie scripts. Once those are all done, assign.features.sense.sh and assign.features.antisense.sh (also created by PIWI_PIPELINE.sh) can be run to get heirarchical counts for features. The counting depends on AssignReadsToFeatures.pl.