- Clone the repository (eg. git clone https://github.com/billytcl/EXB.git).
- Copy
scripts/execute_decoder_qscore.shto 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 thetestfolder for the recommended folder structure. - Edit execute_decoder_qscore.sh and replace
SCRIPTS_DIRvariable to the cloned github folder. Don't include "scripts" in the folder name. - Edit
build_star_genecounts.shso that it points to where STAR is installed. Also change the location to where your STAR reference is located. - Edit
build_rsem.shso that it points to where RSEM is installed. Also change the location to where the RSEM reference is located.
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