My workflow for downloading data from SRA has been the following:
- Access SRA Run Selector.
- Enter the accession number for the project of interest.
- Download "Accession List" for the "Total" data. The accession list is basically, as the name says, a
.txtfile listing all accession numbers for each run in a given bioproject.
- For each accession number in the accession list I run the following command:
$ fastq-dump --accession <accesion_number> --outdir .
How to download data from SRA in Linux systems via the command line? What are fast and scalable ways of achieving this? What should one know before downloading data?
Although there are some similar discussions in this StackExchange (eg. Trying to retrieve sra data using sra explorer, Downloading dataset from SRA (SOLiD Platform), Downloading SRA Files from AWS, etc).
The discussion on What's the best way to download data from the SRA? Is it really this slow? seems like a good starting point, but I wasn't able to find a straightforward guide on how to download data from SRA, e believe that a well thought and complete answer would help beginners alike. I am preparing an answer to the problem myself, but I thought that the community would probably give some interesting insights (: