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Old 07-22-2013, 08:29 AM   #1
Location: Boston

Join Date: Dec 2010
Posts: 10
Default Regenerating CIFs (Cluster Intensity Files)

Hi all. My lab ran a GAIIx flowcell with run parameters set to save and copy images but not Cluster Intensity Files. We really need those CIFs for a custom analysis.

We would try Off-Line Basecalling to recreate the CIFs, but it is very outdated at this point and generates intensity files in a biased format which we can't use.

I have been told by associates that by
  • Moving images back from the network copy location to the local run folder on the instrument,
  • Deleting the BaseCalls folder under Data,
  • Changing the RTAsettings.xml file so that the flags are set to copy and save CIFs.
  • and restarting RTA,
it should be possible to recreate the CIFs from the saved images.

However, when I attempted this, RTA returned an endless stream of "Warning: null color matrix" messages.

Illumina has been of limited use to us on this problem. If anyone knows how to regenerate CIFs from image files using RTA instead of OLB, the information would be hugely appreciated. Thanks!
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