How To Retrieve A .Fastaq File From Sra Using Wget? (And Not Aspera)

Question

[Marina Manrique]

Hi!

I'd like to download a .sra file containing the fastq files for an experiment in the SRA using the wget command. I've been looking for an url to download the files but all I've found is this:

fasp://[e-mail]:22/sra/sra-instant/reads/ByRun/sra/SRR/SRR001/SRR001115/SRR001115.sra/?auth=no&port=33001&bwcap=300000&targetrate=100p&policy=fair&enc=none&lockpolicy=no&locktargetrate=no&lockminrate=no&v=2

that means using Aspera

Anyone knows if I can download the file connecting via FTP or if there's any other way?

Thanks,

marina

[Marina Manrique]

Thanks for the edition Daniel, I forgot to add more tags

Answer 1

[Sean Davis]

Hi, Marina.

The ftp site is here:

ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant

You may want to read some of the details here:

http://www.ncbi.nlm.nih.gov/books/NBK47540/

Hope that helps answer some questions.

Sean

[Kamil]

Your link is broken. Here is a new, working link (24 Nov 2014): http://www.ncbi.nlm.nih.gov/books/NBK158900/

Answer 2

[User 59]

Tip of the hat to Sean, because I looked for it earlier and didn't find it but the equivalent FTP URL for your query is:

ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR001/SRR001115/

so:

wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR001/SRR001115/SRR001115.sra

should do the trick. You need to do the SRA->FASTQ conversion though on the data. The links to the tools, and example command line instructions are in the Download document that Sean linked to.

[Marina Manrique]

Thanks Daniel, just to let people know where to find the info for SRA -> FASTQ conversion http://www.ncbi.nlm.nih.gov/books/NBK47540/#SRA_Download_Guid_B.5_Converting_SRA_for

[Casey Bergman]

@Marina - I had a run-in with this documentation recently, which needs substantial updating... see more here: How To Convert Sra-Lite Paired-End Submission To Fastq?

Answer 3

[Casey Bergman]

Try wget on the following URL template:

http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=dload&run_list=SRRXXXXX&format=fastq

e.g.

wget -O SRR026674.fastq.gz "http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=dload&run_list=SRR026674&format=fastq"

Note: this has horribly slow (~50K/s) download speed, so I would not recommend this for very big files (which effectively all files in SRA are).

Credits: Hat-tip to Stephen Taylor for this via the Galaxy developer's list