By default, SRA files will be downloaded to
~/ncbi/ncbi_public/sra by using sratoolkit from ncbi. However, there is limited space. So I want to change the path. Is there a way to download SRA files using sratoolkit (
fastq-dump) or can I download the SRA files directly without parsing converting it into fastq files?
This is simple! Thanks!
This is super easy, but you still have to extract the FASTQ files from the SRA file using fastq-dump. So it might be just easier to just use fastq-dump, changing the default save directory, according to piet's post.
[UPDATE] Funny enough, just because I posted this, I changed the configuration as by piet's post (which it has worked for me in the past), but now files are still being saved to my home directory for no reason.. gah... downloading SRA files and extracting fastq locally using fastq-dump will probably be the way to move forward.
Unfortunately, NCBI recommends against directly downloading files as of 2019. Basically,