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Did you try changing the sample sheet to specify all 24 TruSeq indexes for lane 3?
The HiScanSQ, like the HiSeq will only allow you to specify index reads or no index reads for the entire run. So you can't turn off collection index cycles for one lane. So, that is not the issue.
Can you post the median qscore plot from SAV for this lane?
Our old sequencer was a HiScanSQ and it was much less able to deal with unbalanced indexes than the HiSeq. (Our HiSeq seems to have zero issues in that regard.) So if you have only a couple of indexes in the lane, it was critical to make sure they were what I called "MK" compliant. That is that each base had both a "C" or "A" AND a "G" or "T". If that is not the case for your indexes, then you may have some very low quality bases that are preventing demultiplexing from occurring.
These can still usually be demultiplexed by telling CASAVA to skip the problematic cycles.
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Phillip
The HiScanSQ, like the HiSeq will only allow you to specify index reads or no index reads for the entire run. So you can't turn off collection index cycles for one lane. So, that is not the issue.
Can you post the median qscore plot from SAV for this lane?
Our old sequencer was a HiScanSQ and it was much less able to deal with unbalanced indexes than the HiSeq. (Our HiSeq seems to have zero issues in that regard.) So if you have only a couple of indexes in the lane, it was critical to make sure they were what I called "MK" compliant. That is that each base had both a "C" or "A" AND a "G" or "T". If that is not the case for your indexes, then you may have some very low quality bases that are preventing demultiplexing from occurring.
These can still usually be demultiplexed by telling CASAVA to skip the problematic cycles.
--
Phillip
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