Step 1: Quality Control (FastQC MultiQC) - rsalani13/EPP622-2026-SNPCalling GitHub Wiki

Commands

cd analyses
mkdir fastqc1
cd fastqc1

#symboloically link reads files
ln -s ../../rawdata/reads/

#make bash script
nano forloop.sh
	
-----------------------------------
     for file in reads/*.fastq.gz
     do
        fastqc -t 2 $file
     done
-----------------------------------

#run the script
Bash forloop.sh

#this runs for a while then outputs a bunch of fastq files!

#run multiqc report
Multiqc .

MultiQC gives a rounded number for total reads and does not report total bases per sample. To find out those numbers...

nano multiqc_analysis.sh

-----------------------------------------------------
     for f in reads/*.fastq.gz; do
       echo -ne "$f\t"
       zcat "$f" | awk 'NR%4==2{r++; b+=length()} END{printf "%d\t%d\t%.1f\n",$
     done | column -t
-----------------------------------------------------

bash multiqc_analysis.sh

This gives the total reads, then the total bases, then the average read length for each file.

Results

MultiQC report path and name: /lustre/isaac24/proj/UTK0505/rsalani/exam2/analyses/fastqc1/multiqc_report.html

Sample	Total reads	Total bases	Quality issues?
A (R1, R2)	1609300	241395000	none
B (R1, R2)	321860	48279000	low coverage
C (R1, R2)	1609300	241395000	polyG
D (R1, R2)	1609300	241395000	low quality