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Old 01-08-2014, 10:58 AM   #5
haroldnunez
Junior Member
 
Location: Chile

Join Date: Jan 2014
Posts: 5
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Quote:
Originally Posted by GenoMax View Post
If you are sure that the index read has worked and for some reason the demultiplexing did not then you can:

a) Try to re-run the analysis with MiSeq reporter or if that does not work
b) try doing the basecalling/demultiplexing using bcltofastq on a separate unix server (for ref: http://seqanswers.com/forums/showthread.php?t=39153)

In any case first see what Tech Support says (I see that you are in Chile but hopefully there is a way to contact the tech support either local or the one in US).
I will try your suggestion, however I'm worried about the quality score. It could improve if I do the basecalling/demultiplexing with bcltofastq? or I just will recover the index?
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