Chapter 3 Prepare the FASTQ dataset

3.1 Download the FASTQ files

The worked example uses ten paired-end RNA-seq samples from PRJNA1161405: Normal1-Normal5 and HCC1-HCC5.

Download the FASTQ files from ENA:

cd "$IOBRPY_DEMO/input/fastq"

curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/060/SRR35344560/SRR35344560_1.fastq.gz -o SRR35344560_Normal1_1.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/060/SRR35344560/SRR35344560_2.fastq.gz -o SRR35344560_Normal1_2.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/061/SRR35344561/SRR35344561_1.fastq.gz -o SRR35344561_Normal2_1.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/061/SRR35344561/SRR35344561_2.fastq.gz -o SRR35344561_Normal2_2.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/062/SRR35344562/SRR35344562_1.fastq.gz -o SRR35344562_Normal3_1.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/062/SRR35344562/SRR35344562_2.fastq.gz -o SRR35344562_Normal3_2.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/063/SRR35344563/SRR35344563_1.fastq.gz -o SRR35344563_Normal4_1.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/063/SRR35344563/SRR35344563_2.fastq.gz -o SRR35344563_Normal4_2.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/064/SRR35344564/SRR35344564_1.fastq.gz -o SRR35344564_Normal5_1.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/064/SRR35344564/SRR35344564_2.fastq.gz -o SRR35344564_Normal5_2.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/066/SRR35344566/SRR35344566_1.fastq.gz -o SRR35344566_HCC1_1.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/066/SRR35344566/SRR35344566_2.fastq.gz -o SRR35344566_HCC1_2.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/067/SRR35344567/SRR35344567_1.fastq.gz -o SRR35344567_HCC2_1.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/067/SRR35344567/SRR35344567_2.fastq.gz -o SRR35344567_HCC2_2.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/068/SRR35344568/SRR35344568_1.fastq.gz -o SRR35344568_HCC3_1.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/068/SRR35344568/SRR35344568_2.fastq.gz -o SRR35344568_HCC3_2.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/069/SRR35344569/SRR35344569_1.fastq.gz -o SRR35344569_HCC4_1.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/069/SRR35344569/SRR35344569_2.fastq.gz -o SRR35344569_HCC4_2.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/070/SRR35344570/SRR35344570_1.fastq.gz -o SRR35344570_HCC5_1.fastq.gz
curl -L \
  ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR353/070/SRR35344570/SRR35344570_2.fastq.gz -o SRR35344570_HCC5_2.fastq.gz

The output directory contains:

$IOBRPY_DEMO/input/fastq/
├── SRR35344560_Normal1_1.fastq.gz
├── SRR35344560_Normal1_2.fastq.gz
├── SRR35344561_Normal2_1.fastq.gz
├── SRR35344561_Normal2_2.fastq.gz
├── SRR35344562_Normal3_1.fastq.gz
├── SRR35344562_Normal3_2.fastq.gz
├── SRR35344563_Normal4_1.fastq.gz
├── SRR35344563_Normal4_2.fastq.gz
├── SRR35344564_Normal5_1.fastq.gz
├── SRR35344564_Normal5_2.fastq.gz
├── SRR35344566_HCC1_1.fastq.gz
├── SRR35344566_HCC1_2.fastq.gz
├── SRR35344567_HCC2_1.fastq.gz
├── SRR35344567_HCC2_2.fastq.gz
├── SRR35344568_HCC3_1.fastq.gz
├── SRR35344568_HCC3_2.fastq.gz
├── SRR35344569_HCC4_1.fastq.gz
├── SRR35344569_HCC4_2.fastq.gz
├── SRR35344570_HCC5_1.fastq.gz
└── SRR35344570_HCC5_2.fastq.gz

3.2 Check the FASTQ files

test "$(find "$IOBRPY_DEMO/input/fastq" -maxdepth 1 -name '*.fastq.gz' | wc -l)" -eq 20
gzip -t "$IOBRPY_DEMO"/input/fastq/*.fastq.gz
echo "All twenty FASTQ files passed the gzip integrity check."

Data source: NCBI BioProject PRJNA1161405.