We've encountered a problem with the last couple of paired end, dual indexed runs on our HiSeq 2500 and I wanted to check if any others have had similar experience. The problem is that the signal intensity and thus the read quality of Index read #2 is very poor. All other aspects of the run, meaning Read 1, Index 1 and Read 2 work perfectly fine, good signal and quality. The poor quality of Index #2 results in problems with demultiplexing.
We have run a couple of single read, dual index runs and in those cases index read 2 is fine, of course the manner in which index read 2 is done on single read vs paired end read flow cells differs.
We contacted Illumina and they have no explanation. Nothing stood out in the log files to suggest a cause. The engineer did some back flushing and checking of the fluidics but we have not tested it since that was done.
Does this sound familiar to anyone? Any ideas would be appreciated as well.
We have run a couple of single read, dual index runs and in those cases index read 2 is fine, of course the manner in which index read 2 is done on single read vs paired end read flow cells differs.
We contacted Illumina and they have no explanation. Nothing stood out in the log files to suggest a cause. The engineer did some back flushing and checking of the fluidics but we have not tested it since that was done.
Does this sound familiar to anyone? Any ideas would be appreciated as well.
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