Chapter 3 Prepare the FASTQ dataset

3.1 Download the FASTQ files

Download the complete paired-end FASTQ files from ENA:

mkdir -p data/fastq

wget -c https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR503/DRR503996/DRR503996_1.fastq.gz -P data/fastq
wget -c https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR503/DRR503996/DRR503996_2.fastq.gz -P data/fastq
wget -c https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR503/DRR503997/DRR503997_1.fastq.gz -P data/fastq
wget -c https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR503/DRR503997/DRR503997_2.fastq.gz -P data/fastq
wget -c https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR503/DRR503998/DRR503998_1.fastq.gz -P data/fastq
wget -c https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR503/DRR503998/DRR503998_2.fastq.gz -P data/fastq
wget -c https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR503/DRR503999/DRR503999_1.fastq.gz -P data/fastq
wget -c https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR503/DRR503999/DRR503999_2.fastq.gz -P data/fastq
wget -c https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR504/DRR504000/DRR504000_1.fastq.gz -P data/fastq
wget -c https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR504/DRR504000/DRR504000_2.fastq.gz -P data/fastq
wget -c https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR504/DRR504001/DRR504001_1.fastq.gz -P data/fastq
wget -c https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR504/DRR504001/DRR504001_2.fastq.gz -P data/fastq

The output directory contains:

data/fastq/
├── DRR503996_1.fastq.gz
├── DRR503996_2.fastq.gz
├── DRR503997_1.fastq.gz
├── DRR503997_2.fastq.gz
├── DRR503998_1.fastq.gz
├── DRR503998_2.fastq.gz
├── DRR503999_1.fastq.gz
├── DRR503999_2.fastq.gz
├── DRR504000_1.fastq.gz
├── DRR504000_2.fastq.gz
├── DRR504001_1.fastq.gz
└── DRR504001_2.fastq.gz

3.2 Check the FASTQ files

test "$(find data/fastq -maxdepth 1 -name '*.fastq.gz' | wc -l)" -eq 12
gzip -t data/fastq/*.fastq.gz
echo "All twelve FASTQ files passed the gzip integrity check."

Data source: ENA study PRJDB16684.