Question

Downloading Ncbi Query Results Using Aspera?

0

Entering edit mode

11.2 years ago

edwardbeaty • 0

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.

ncbi aspera • 3.0k views

ADD COMMENT • link updated 9.8 years ago by Casey Bergman 18k • written 11.2 years ago by edwardbeaty • 0

score 1 · Answer 1 · 2013-02-21

1

Entering edit mode

11.2 years ago

Istvan Albert 100k

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 COMMENT • link 11.2 years ago by Istvan Albert 100k

score 0 · Answer 2 · 2013-02-27

0

Entering edit mode

11.1 years ago

Cliff Beall ▴ 470

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 COMMENT • link 11.1 years ago by Cliff Beall ▴ 470

score 0 · Answer 3 · 2013-02-27

0

Entering edit mode

11.1 years ago

Jeremy Leipzig 22k

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 COMMENT • link 11.1 years ago by Jeremy Leipzig 22k