02. Quality Checking

Check the quality scores in the fastq files.

Input Files

ls Sample_reads

10_S10_L001_R1_001.fastq.gz

10_S10_L001_R2_001.fastq.gz

11_S11_L001_R1_001.fastq.gz

11_S11_L001_R2_001.fastq.gz

Command

bash Scripts/2-fastqc_reports.sh

Ouputs

The above script will create Fastqc_Report folder.

• Fastqc_Reports -The output folder
• .html - The quality summary of each sample
• multiqc_report.html - The overall summary of the samples, created by multiqc.