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Old 12-11-2008, 05:05 AM   #1
Location: Malmö

Join Date: Sep 2008
Posts: 37
Default running out of disk space (Solexa)


In my group we have a Solexa machine and we are having problems in saving all data generated by a run. Until now I have been using only the fastq files and some report files but nothing else. (I know that public databases like GEO can accept only fastq files:

Questions: Is it ok to remove all the other files for good? Do they retain any important information that fastq files cannot give?

All comments are appreciated.
Best regards.
fadista is offline   Reply With Quote
Old 12-11-2008, 10:29 AM   #2
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Location: San Diego

Join Date: May 2008
Posts: 912

Some people are keeping every scrap of data, but I think that lots of labs are, for space reasons, tossing most of the intermediate files.

The new IPAR set-up automatically tosses the images, I think, unless you set up some pipeline to store them elsewhere. In theory, the intensity files could be run through alterante pipelines, like Alta-cyclic, so there might be a reason to hang onto those, but what are the odds of you actually doing that with most of your data?

I know I'd feel a bit safer with the whole Gerald folder, or maybe keeping the .prb files and the .seq files too, so you can remake the fastq, if you had to.
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Old 12-11-2008, 11:50 AM   #3
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Location: Woodbridge CT

Join Date: Oct 2008
Posts: 231
Default blobs anyone?

see bloby images at

what others say at

Save all data=quality control, unexpected discrepancy resolution between experiments and labs. Resequence vs reanalyze? What if there is no more sample?
Joann is offline   Reply With Quote


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