How to convert to .SRA files to .FQ (FASTQ)

Question

[Mariana]

Hello everyone,

I'm trying to convert SRR10513216 files to fastq form.

fastq-dump SRR10513216.sra
fastq-dump --split-files -A SRR10513216.sra

But I am getting an error which says the following

fastq-dump.2.8.0 err: item not found while constructing within virtual database module - the path 'SRR10513216.sra' cannot be opened as database or table.

Could anyone please tell me how to resolve this? It would be of great help!

[petebio]

Another option rather than using fastq-dump would be to download the fastq files directly. You can find the url for these using ffq

ffq --ftp SRR10513216

This will give you the direct URLs for the fastq files that can be downloaded using something like wget. This is often quicker and more straightforward than using fastq-dump.

Answer 1

[GenoMax]

Have you pre-fetched the SRA file?

Otherwise you should do

fastq-dump -F --split-files SRR10513216