3 Downloading Multiple Fastq Files

To download multiple fastq files, follow these steps:

3.1 Confirm fasterq-dump Installation

Ensure that fasterq-dump is in the path. You can type which fasterq-dump or fasterq-dump --help in the terminal to confirm its presence.

3.2 Specify Output and Temporary Files

When using fasterq-dump, you must specify the output directory (--outdir) and temporary directory (--temp).

3.3 Download in a Loop

You can use a for loop to specify a range of SRA accessions and download them sequentially. Here’s an example code for downloading reads from the NCBI-SRA for accessions ranging from SRR7450706 to SRR7450761:

for (( i = 706; i <= 761; i++ ))
    do
        time fasterq-dump SRR7450$i \
        --split-3 \
        --force \
        --skip-technical \
        --outdir data/reads \
        --temp data/temp \
        --threads 4     
    done