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==== Quality Control with FastQC, Fastp and 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.

=== FastQC ===

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>

== Parent script ==
fastqc_00.sh
<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_00
#SBATCH --output=log/fastqc_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_00
#SBATCH --output=log/multiqc_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_00
#SBATCH --output=log/multiqc_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>

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