EXB

processing scripts for EXB workflow

Instructions:

• Clone the repository (eg. git clone https://github.com/billytcl/EXB.git).
• Copy scripts/execute_decoder_qscore.sh to an analysis folder of your choice.
• Create a folder inside the analysis directory named fastq. Copy the fastq files inside, ensuring that they are in the name format *.fq.gz. See the test folder for the recommended folder structure.
• Edit execute_decoder_qscore.sh and replace SCRIPTS_DIR variable to the cloned github folder. Don't include "scripts" in the folder name.
• Edit build_star_genecounts.sh so that it points to where STAR is installed. Also change the location to where your STAR reference is located.
• Edit build_rsem.sh so that it points to where RSEM is installed. Also change the location to where the RSEM reference is located.