Download raw fastq files from SRA with sra tools

fetch_fastq.sh

# Taken from https://www.biostars.org/p/111040/
# Examine and save metadata 
esearch -db sra -query PRJNA484081  | efetch -format runinfo > bioproj.csv

# The first column of comma separated runinfo file are run ids
cat bioproj.csv | cut -d ',' -f 1 | head

# Download first 4 files as an example
cat bioproj.csv | cut -d ',' -f 1 | grep 'SRR' # Check of we are selecting right files

# Download the files
cat bioproj.csv | cut -d ',' -f 1 | grep 'SRR' | xargs fastq-dump --split-files

# Run in parallel
cat bioproj.csv | cut -d ',' -f 1 | grep 'SRR' | xargs -n 1 -P 12 fastq-dump --split-files --gzip --skip-technical