Begins to re-factor scripts for executable analyses
Updates bowtie version and filenames
Updates read count script
Changes read counts folder
Import function updated
Normalize shell script
Just adds set option
Fixes STEM input files
Import stem updated
Somehow working plots, but need more adjustments
Properly fixes plot building
Reviews and fixes all scripts, stem in the end
Make adjustments to analysis text
Adds wait command to control the main script
Fixes links and order of pipeline
Moves folder with read counts
Fixes links of mains scripts
Another typo
Updates bowtie2 commands
Fixes object name