Fastqc

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
Posted in How-To-Guides, HPC
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