FastQC, Trimming, Overall QC (initial)

This commit is contained in:
Jos van Nijnatten
2021-02-09 12:52:44 +01:00
parent 7ecbc2aee9
commit 3d7c9e3b1c
9 changed files with 988 additions and 0 deletions

View File

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#!/bin/bash
#SBATCH --job-name=fastqc
#SBATCH --time=0-12:00:00
#SBATCH --ntasks=1
#SBATCH --mem=15G
#SBATCH --qos=regular
set -e
set -u
set -x
set -o pipefail
module purge
module load Java
module load FastQC
dir_raw_fastq="$(pwd)/fastq/raw"
dir_fastqc="$(pwd)/fastqc"
[ -d "${dir_fastqc}" ] || mkdir -p "${dir_fastqc}"
# Run FastQC
files=$(find -L "$dir_raw_fastq" -type f -iname "*.fastq.gz")
for file in $files; do
filename=$(basename "$file")
fastqc -o "$dir_fastqc" "$file" &
done
wait