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Old 05-23-2014, 08:20 AM   #3
skerker
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Location: CA

Join Date: Nov 2009
Posts: 10
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Thank you for the reply! You did magbead cleanup of the SMRTbell library? I have been submitting samples to a sequence center, so unfortunately I don't have much control over what gets done, or what steps failed. I am trying to get more information to help troubleshoot my experiment.

It seems to me that the original gDNA can be cleaned up further - using powerclean Pro kit form MoBio, or do additional cleanup of the final library.
Do you have a feeling for which approach is better?

The initial cleanup I can do - the latter would have to be done by the PacBio sequencing provider, but I could suggest that they do the additional cleanup step.

I found some posters from PacBio on the subject. I think they tried a few different cleanup methods (magbead, qiaquick, etc). So perhaps this is a common problem and should always be done as a final cleanup of the library before sequencing?

Are you part of a PacBio sequence center? If so, I could submit my samples to your center so at least I know they would be cleaned up if a problem arises? Or maybe suggest a center that you have had good success with?

Thanks again,

Jeff
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