2. Added updated alignments params for 101bp paired-end RNA-Seq data
3. Updated sequencing application codes to include new applications and removed outdated ones
4. Updated miRNA alignment params
5. Removed code to make the QC, processedAlignments, and coverageTracks dirs in GNomEx, as it appears that most users delete them and make their own
6. Changed dir path of tomato/job/ to /tomato/dev/job/ to work with Tomato3
7. Changed path of autoalignerData to /tomato/dev/job/autoaligner/autoalignerData/
8. Changed path of apps to /tomato/dev/job/autoaligner/apps/
9. Changed the number of lines in each split bisulfite fastq file to cut down on file #
