Hi everyone,
We are consistently seeing an issue on our MiSeq where Read 1 has very poor Q30 scores, followed by a successful sequencing of Read 2 with Q30 scores above 80%. We have had successful runs where we didn't see this trend but it seems about every other run we see this happening. We have talked with Illumina Tech Support and they don't seem to know what is going on. They adjusted the temperature of the instrument (set it a few degrees lower) but this didn't seem to fix the issue. Has anyone else had similar issues? Any insight would be much appreciated.
Thanks! See below for run specifics:
Chemistry: Miseq v3 600 cycle kit.
Read configurations: R1 = 150 cycles, Index = 16 cycles, R2 = 150 cycles.
The library is a DNA hybridization capture, with avg library length ~320 bases
The library was run with 10% PhiX spike-in.
Custom primers were NOT used.
We are consistently seeing an issue on our MiSeq where Read 1 has very poor Q30 scores, followed by a successful sequencing of Read 2 with Q30 scores above 80%. We have had successful runs where we didn't see this trend but it seems about every other run we see this happening. We have talked with Illumina Tech Support and they don't seem to know what is going on. They adjusted the temperature of the instrument (set it a few degrees lower) but this didn't seem to fix the issue. Has anyone else had similar issues? Any insight would be much appreciated.
Thanks! See below for run specifics:
Chemistry: Miseq v3 600 cycle kit.
Read configurations: R1 = 150 cycles, Index = 16 cycles, R2 = 150 cycles.
The library is a DNA hybridization capture, with avg library length ~320 bases
The library was run with 10% PhiX spike-in.
Custom primers were NOT used.
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