Question: How To Retrieve A .Fastaq File From Sra Using Wget? (And Not Aspera)
7
gravatar for Marina Manrique
9.1 years ago by
Marina Manrique1.3k
Granada
Marina Manrique1.3k wrote:

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://anonftp@ftp-private.ncbi.nlm.nih.gov: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

sra fastq retrieval • 19k views
ADD COMMENTlink modified 9.0 years ago by Casey Bergman18k • written 9.1 years ago by Marina Manrique1.3k

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

ADD REPLYlink written 9.1 years ago by Marina Manrique1.3k
8
gravatar for Sean Davis
9.1 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

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

ADD COMMENTlink modified 3.3 years ago by Istvan Albert ♦♦ 82k • written 9.1 years ago by Sean Davis26k
1

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

ADD REPLYlink written 5.2 years ago by Kamil2.0k
6
gravatar for Daniel Swan
9.1 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

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.

ADD COMMENTlink modified 5 months ago by RamRS25k • written 9.1 years ago by Daniel Swan13k

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

ADD REPLYlink modified 5 months ago by RamRS25k • written 9.1 years ago by Marina Manrique1.3k

@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?

ADD REPLYlink modified 5 months ago by RamRS25k • written 8.5 years ago by Casey Bergman18k
0
gravatar for Casey Bergman
8.5 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

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

ADD COMMENTlink modified 5 months ago by RamRS25k • written 8.5 years ago by Casey Bergman18k
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