sratoolkit and download

Question

[qudrat]

Hello all,

I have been trying to download a .sra file of 20GB using "wget" and "curl" command but due to bad connectivity of internet I am unable to download. I also tryied prefetch and fastq-dump but it did not work (it did work for smaller file). Please suggest me how to proceed.

Thank you

Answer 1

[grant.hovhannisyan]

Try to install aspera utility https://www.ncbi.nlm.nih.gov/books/NBK158899/#SRA_download.accessing_the__ascp_utility, then prefetch the sra file (in my experience prefetch is more stable than fastq-dump), and once it is downloaded use fastq-dump.

EDIT: Also you can try to find that dataset in ENA database and try to download fastq files directly.