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--- scripts:qc [2025/03/11 11:41] – created 37.26.174.181
+++ scripts:qc [2025/03/21 12:43] (current) – 37.26.174.181
@@ Line 1: / Line 1: @@
-====== Perform quality check of your FASTQ files ======
+==== Quality Control with FastQC, Fastp and MultiQC ====
-===== QC with FASTQC & MULTIQC =====
+The following scripts perform quality check with FastQC and MultiQC. You can find Fastp in [[scripts:adapter_and_quality_trimming|How to perform quality control and adapter trimming of your reads with cutadapt and fastp]]. Fastp performs quality trimming and also generates reports, which can be used as input to MultiQC.
-==== Daughter script ====
+=== FastQC ===
-==== Parent script ====
+Uses fastq files as inputs and generates reports. Below daughter and parent scripts are provided.
+== Dauther script ==
+fastqc.sh
 <code>
+# SCRIPT FOR PERFORMING FASTQC
+# NOTE: Run this script from the directory where the "log" directory is located,
+#       Example: /mnt/proj/ibd/ds-06_cd-fecal/common
+#
+# PURPOSE:
+#   This script performs FastQC.
+#
+# PARAMETERS:
+#   1: input_dir - Directory where FASTQ files are located.
+#   2: output_dir - Directory where FastQC reports will be located
+# SAMPLE USAGE:
+#   In a parent script: src/fastqc.sh <input_dir> <output_dir>
+#
+# IMPORTANT:
+#   - Run from a parent script.
+# Check if correct number of arguments are provided
+if [ "$#" -ne 2 ]; then
+    echo "Usage: $0 <input_dir> <output_dir>"
+    exit 1
+fi
+# Input parameters
+input_dir="$1"
+output_dir="$2"
+echo "Running FastQC on reads..."
+mkdir -p "$output_dir"
+fastqc -o "$output_dir" "$input_dir/"*.fq.gz
 </code>
-===== QC with FASTP & MULTIQC =====
+== Parent script ==
-==== Daughter script ====
+fastqc_00.sh
-==== Parent script ====
+<code>
+#!/bin/bash
+#SBATCH --mem=10gb
+#SBATCH --cpus-per-task=10
+#SBATCH --job-name=fastqc_00
+#SBATCH --output=log/fastqc_00%j.log  # %j will be replaced with the job ID
+#parameters
+input=fq_renamed
+output=fastqc
+src/fastqc.sh $input $output
+</code>
+=== MultiQC ===
+MultiQC generates a report based on multiple FastQC reports and enables to view then simultaneously. MultiQC also takes Fastp reports as input and allocates a separate section.
+== Dauther script ==
+multiqc.sh
+<code>
+# SCRIPT FOR PERFORMING MultiQC
+# NOTE: Run this script from the directory where the "log" directory is located,
+#       Example: /mnt/proj/ibd/ds-06_cd-fecal/common
+#
+# PURPOSE:
+#   This script performs MultiQC.
+#
+# PARAMETERS:
+#   1: input_dir - Directory where FastQC reports are located.
+#   2: output_dir - Directory where MultiQC report will be located
+# SAMPLE USAGE:
+#   In a parent script: src/multiqc.sh <input_dir> <output_dir>
+#
+# IMPORTANT:
+#   - Run from a parent script.
+# Check if correct number of arguments are provided
+if [ "$#" -ne 2 ]; then
+    echo "Usage: $0 <input_dir> <output_dir>"
+    exit 1
+fi
+# Input parameters
+input_dir="$1"
+output_dir="$2"
+echo "Running MultiQC..."
+mkdir -p "$output_dir"
+multiqc -o "$output_dir" "$input_dir"
+</code>
+== Parent script ==
+multiqc_00.sh
+<code>
+#!/bin/bash
+#SBATCH --mem=10gb
+#SBATCH --cpus-per-task=10
+#SBATCH --job-name=multiqc_00
+#SBATCH --output=log/multiqc_00%j.log  # %j will be replaced with the job ID
+#parameters
+input=fastqc
+output=multiqc
+src/multiqc.sh $input $output
+</code>
+You can also perform them simultaneously with one parent script:
+== Combined parent script ==
+qc_00.sh
+<code>
+#!/bin/bash
+#SBATCH --mem=10gb
+#SBATCH --cpus-per-task=10
+#SBATCH --job-name=fastqc_multiqc_00
+#SBATCH --output=log/fastqc_multiqc_00%j.log  # %j will be replaced with the job ID
+#parameters
+input_fqc=fq
+output_fqc=fastqc
+input_mqc=fastqc
+output_mqc=multiqc
+src/fastqc.sh $input_fqc $output_fqc
+src/multiqc.sh $input_mqc $output_mqc
+</code>
+You can also use the same scripts on trimmed files. Just add "_trimmed" to the inputs and outputs like this. Remember to save them in separate folders (fastqc_trimmed, multiqc_trimmed)
+fastqc_post_00.sh
+<code>
+#!/bin/bash
+#SBATCH --mem=10gb
+#SBATCH --cpus-per-task=10
+#SBATCH --job-name=fastqc_post_00
+#SBATCH --output=log/fastqc_post_00%j.log  # %j will be replaced with the job ID
+#parameters
+input=fq_trimmed
+output=fastqc_trimmed
+src/fastqc.sh $input $output
+</code>
+multiqc_post_00.sh
+<code>
+#!/bin/bash
+#SBATCH --mem=10gb
+#SBATCH --cpus-per-task=10
+#SBATCH --job-name=multiqc_post_00
+#SBATCH --output=log/multiqc_post_00%j.log  # %j will be replaced with the job ID
+#parameters
+input=fastqc_trimmed
+output=multiqc_trimmed
+src/multiqc.sh $input $output
+</code>
+=== Fastp ===
+If you want to add Fastp reports to MultiQC, you can add "fq_trimmed" directory as input to MultiQC (multiqc_fastp.sh).
+== Daughter script ==
+multiqc_fastp.sh:
+<code>
+# SCRIPT FOR PERFORMING MultiQC
+# NOTE: Run this script from the directory where the "log" directory is located,
+#       Example: /mnt/proj/ibd/ds-06_cd-fecal/common
+#
+# PURPOSE:
+#   This script performs MultiQC.
+#
+# PARAMETERS:
+#   1: input_dir - Directory where FastQC reports are located.
+#   2: output_dir - Directory where MultiQC report will be located
+# SAMPLE USAGE:
+#   In a parent script: src/multiqc.sh <input_dir> <output_dir>
+#
+# IMPORTANT:
+#   - Run from a parent script.
+# Check if correct number of arguments are provided
+if [ "$#" -ne 2 ]; then
+    echo "Usage: $0 <input_dir> <output_dir>"
+    exit 1
+fi
+# Input parameters
+input_dir=$1
+input_fastp=$2
+output_dir=$3
+echo "Running MultiQC..."
+mkdir -p "$output_dir"
+multiqc -o "$output_dir" "$input_dir" "$input_fastp"
+</code>
+== Parent ==
+multiqc_fastp_00.sh
+<code>
+#!/bin/bash
+#SBATCH --mem=10gb
+#SBATCH --cpus-per-task=10
+#SBATCH --job-name=multiqc_fastp_00
+#SBATCH --output=log/multiqc_fastp_00%j.log  # %j will be replaced with the job ID
+#parameters
+input=fastqc_trimmed
+input_fastp=fq_trimmed
+output=multiqc_trimmed
+src/multiqc.sh $input $input_fastp $output
+</code>