Question: Downloading Ncbi Query Results Using Aspera?
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gravatar for edwardbeaty
6.5 years ago by
edwardbeaty0 wrote:

Hi, all. I have a very large result set (150k results) from NCBI Entrez that I want to download as genbank files. I just found the Aspera plugin for file transfer...does anyone know if it's possible to download very large query results using this tool? Thanks.

aspera ncbi • 2.0k views
ADD COMMENTlink modified 5.2 years ago by Casey Bergman18k • written 6.5 years ago by edwardbeaty0
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gravatar for Istvan Albert
6.5 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

AFAIK the aspera tool is for uploading/downloading large datasets that exist as separate files on disk. The results of dynamically generated queries do not exist in such a form.

ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by Istvan Albert ♦♦ 81k
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gravatar for Cliff Beall
6.5 years ago by
Cliff Beall450
Ohio
Cliff Beall450 wrote:

There is a command-line version (ascp), maybe you could incorporate it in a script?

http://www.ncbi.nlm.nih.gov/books/NBK47527/ also: http://betascience.blogspot.com/2010/02/using-aspera-instead-of-ftp-to-download.html

ADD COMMENTlink written 6.5 years ago by Cliff Beall450
0
gravatar for Jeremy Leipzig
6.5 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

I couldn't even make ascp accept wildcards, although the documentation suggests it is possible. Basically you need to know which files you want a priori.

ADD COMMENTlink written 6.5 years ago by Jeremy Leipzig18k
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