SRA data submission

amstisla · 03-12-2009, 09:25 AM

Does the anybody have experience in Illumina data submission to the Short Read Archive? I feel a little frustration after reading official documentation...
I've already created srf files, but have no ideas about xml (.experiment.xml, .run.xml, .sample.xml and study.xml). Are some special xml tools exists to generate it based on xsd schemas? Or it is expected to do this manually? Did you use ftp or proposed fasp protocol from Aspera for data transfer?

Thanks, Slava

bioinfosm · 03-12-2009, 02:38 PM

There is an sra submission tool from WashU St Louis.. The guy had a poster at AGBT

idas · 06-14-2010, 09:11 AM

I think you maybe describing the poster that was given at AGBT 2009, by The Genome Center at Washington University in St. Louis. It is available for viewing via github at:

http://github.com/indraniel/agbt2009...f/agbt2009.pdf

The poster is not describing any particular tool, but rather an implementation of an automated system developed at the Genome Center.

There is some additional information/discussion about the poster at the following blog post as well:

http://www.politigenomics.com/2009/01/sra-at-agbt.html

Feel free to let us know if anyone has any questions about the system.

Sincerely,
Indraniel Das

The Genome Center at Washington University

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03-12-2009, 09:25 AM	#1
amstisla Junior Member Location: Berlin Join Date: Aug 2008 Posts: 4	SRA data submission Does the anybody have experience in Illumina data submission to the Short Read Archive? I feel a little frustration after reading official documentation... I've already created srf files, but have no ideas about xml (.experiment.xml, .run.xml, .sample.xml and study.xml). Are some special xml tools exists to generate it based on xsd schemas? Or it is expected to do this manually? Did you use ftp or proposed fasp protocol from Aspera for data transfer? Thanks, Slava Last edited by amstisla; 03-12-2009 at 09:27 AM.

06-14-2010, 09:11 AM	#3
idas Junior Member Location: St. Louis, MO USA Join Date: Mar 2010 Posts: 3	The Genome Center at Washington University SRA submissions system (AGBT 2009 poster) I think you maybe describing the poster that was given at AGBT 2009, by The Genome Center at Washington University in St. Louis. It is available for viewing via github at: http://github.com/indraniel/agbt2009...f/agbt2009.pdf The poster is not describing any particular tool, but rather an implementation of an automated system developed at the Genome Center. There is some additional information/discussion about the poster at the following blog post as well: http://www.politigenomics.com/2009/01/sra-at-agbt.html Feel free to let us know if anyone has any questions about the system. Sincerely, Indraniel Das The Genome Center at Washington University

03-12-2009, 02:38 PM	#2
bioinfosm Senior Member Location: USA Join Date: Jan 2008 Posts: 482	There is an sra submission tool from WashU St Louis.. The guy had a poster at AGBT