Main directory: /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/matt_transcriptome
Folder 1: rawdata
Fastq: contains all the raw fastq files for 12 samples (paired end reads).
RNA_Lycaeides_Melissa2018: contains count files and extra files sent by Josh.
Folder 2: parsed
Contains output files after phiX filtering
Folder 3: reference
Folder 4: trim_galore
Folder 5: txome_assembly
Folder 6: cufflinks
Folder 7: tophat-2.1.1.Linux_x86_64