Fastqc is a quality control tool for high throughput sequence data.
It may be started from a remote desktop session on koko-login.hpc.fau.edu using the following terminal commands.
Batch Job:
Create a file named fastqc.sh and paste the following into it. Now execute the job using sbatch fastqc.shi.
#!/bin/bash #SBATCH -c 20 #SBATCH -C intel #SBATCH -p longq7 module load jdk-12.0.2_10-gcc-8.3.0-2wddza7 module load fastqc # PATH TO FQ files FQFILES="~/fastqcfilespath/" cd $FQFILES fastqc *.fq
Interactive Usage:
ssh localhost -Y salloc -c 20 -C intel --x11 -p shortq7 module load fastqc module load jdk-12.0.2_10-gcc-8.3.0-2wddza7 srun fastqc *.fq
X11 Usage:
ssh localhost -Y salloc -c 20 -C intel --x11 -p shortq7 module load fastqc module load jdk-12.0.2_10-gcc-8.3.0-2wddza7 srun fastqc