You've loaded an old revision of the document! If you save it, you will create a new version with this data. Media Files==== 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 $output </code> == Dauther script == multiqc.sh <code> # SCRIPT FOR PERFORMING MultiQC # NOTE: Run this script from the directory where the "log" directory is located, # Example: /mnt/proj/ibd/ds-06_cd-fecal/common # # PURPOSE: # This script performs MultiQC. # # PARAMETERS: # 1: input_dir - Directory where FastQC reports are located. # 2: output_dir - Directory where MultiQC report will be located # SAMPLE USAGE: # In a parent script: src/multiqc.sh <input_dir> <output_dir> # # IMPORTANT: # - Run from a parent script. # Check if correct number of arguments are provided if [ "$#" -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/"*.fq.gz </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. == Parent script == multiqc_00.sh <code> #!/bin/bash #SBATCH --mem=10gb #SBATCH --cpus-per-task=10 #SBATCH --job-name=fastqc_multiqc_00 #SBATCH --output=log/fastqc_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 == fastqc_multiqc_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 olders (fastqc_trimmed, multiqc_trimmed) <code> #Input parameters input=fq_trimmed output=fastqc_trimmed </code> == Fastp == If you want to add Fastp reports to MultiQC, you can add "fq_trimmed" directory as input to MultiQC. In daughter script: <code> # Rest of the code # Input parameters input_dir="$1" input_fastp="$2" output_dir="$3" # Rest of the code </code> In parent script: <code> # Rest of the code src/multiqc.sh $input_dir $input_fastp $output_dir </code>SavePreviewCancel Edit summary
