Quality control

Source the configuration file:

source conf_cluster.conf

FastQC provides a report of the quality of your Illumina sequences. First, create a directory to save the results of the quality check:

mkdir -p $wd/$PRJ_NAME/0_QualityControl

Load fastqc module:

module load profile/advanced
module load profile/bioinf
module load autoload fastqc

Run FastQC:

for i in $SAMPLE_LIST; do fastqc -o $wd/$PRJ_NAME/0_QualityControl --nogroup $INPUT_DIR/$i.R1.fastq $INPUT_DIR/$i.R2.fastq; done

In a shell of YOUR COMPUTER, create a directory and copy the FastQC output:

mkdir -p ~/icme9/fqc-results
cd ~/icme9/fqc-results
scp userneme@login.galileo.cineca.it:/path/to/quality_control/*html .