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I have a hiseq run and in Lanes 2, 4, and 6 I have Ns at base 18 in all sequences. Similar library types are run in other lanes and do not have this problem. Anyone have any reasons why this could happen?
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This almost certainly indicates a fluidics or camera (focusing) problem associated with those lanes at cycle 18. If you see N's for only a portion of the reads in a lane for a cycle (e.g. only the top or bottom surface, or just one swath) then the problem is almost certainly a focus problem. Focus problems can result from the presence of an air bubble in the lane near the inlet port where the scanner focuses before each swath. I suppose it is possible that these lanes each had such a large bubble it destroyed focus for all swaths on both surfaces. However the instrument pumps new scan reagent between scanning the top and bottom surface so that seems unlikely.Originally posted by SLB View Post
Contact Illumina Tech Support (or have your sequencing core do so) and have them look at the run data (stored in the InterOp folder).
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