Access to fastq files on SRA Run browser

Question

[Chintan]

Hi, as I was looking for sources to access fastq files directly instead of converting them from .sra and avoid the use of the SRA toolkit, I came across these links on the run browser which have aws s3 bucks links to fastq files but for some reason they are not made public or need lot of permissions to access. Can someone please give me more info on this on why this is the way it is? example image, fastq files under the "Original format" below

[biofalconch]

Seems like you need to apply for access to this dataset due to them being from humans

"The dbGaP data are organized into consent groups which consist of all the data from study participants who have agreed to the same data use as specified in the informed consent for the study. Data access is only approved in unit of consent group, and, therefore data requestors should understand the Data Use Limitations (DULs) of a consent group prior to applying for dbGaP data access"

You can of course apply for access, read more about it here: https://www.ncbi.nlm.nih.gov/books/NBK570242/

[GenoMax]

This particular SRR accession is public. No dbGaP needed.

Answer 1

[ATpoint]

I don't see the issue. The fastq files are in an Amazon S3 bucket, so you could download them from there. I am not much into aws but afaik you need some sort of amazon toolkit for this.

Alternatively (and my recommendation), enter the accessions at sra-explorer.info and get ftp download links for fastq files.

[ATpoint]

I also heard good things about https://github.com/rpetit3/fastq-dl which automates the query and download.

Answer 2

[xiaoguang]

A more straightforward way to get any public data is using the prebuilt pipeline from nf-core.

the link is:

https://nf-co.re/fetchngs/1.10.1