Dear colleagues!
We have conducted a HiSeq 2500 dual index paired end run using TruSeq SBS Kit v3 - HS (200-cycles) chemistry and TruSeq PE Cluster Kit v3 - cBot – HS cluster generation kit for libraries prepared with Nextera Rapid Capture Exome. We had 93-8-8-93 cycles, but it seems like we had not enough ICB for the first part of the run due to an error with ICB splitting. So, we have very degraded data for cycles 102-111, including cycles 102-109 for the Index 2 reads. The amount of Q30 nucleotides for Index 2 read is about 0,1%.
Is it worth trying to get any info for the index 2 reads out of such a run to demultiplex the samples?
I believe there are no chances, but I must use any possibility to minimize the losses.
We have conducted a HiSeq 2500 dual index paired end run using TruSeq SBS Kit v3 - HS (200-cycles) chemistry and TruSeq PE Cluster Kit v3 - cBot – HS cluster generation kit for libraries prepared with Nextera Rapid Capture Exome. We had 93-8-8-93 cycles, but it seems like we had not enough ICB for the first part of the run due to an error with ICB splitting. So, we have very degraded data for cycles 102-111, including cycles 102-109 for the Index 2 reads. The amount of Q30 nucleotides for Index 2 read is about 0,1%.
Is it worth trying to get any info for the index 2 reads out of such a run to demultiplex the samples?
I believe there are no chances, but I must use any possibility to minimize the losses.
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