I recently ran a ~400bp library prepped with NexteraXT on the MiSeq using reagents kit v3 for a 2x300 run. The project was DeNovo Assembly, paired end single index. I got high but in range cluster densities of 1383k/mm2 with 88.2% passing filter.
My issue is that the run only had 43% >Q30 bases. Does anyone have any ideas for troubleshooting?
My issue is that the run only had 43% >Q30 bases. Does anyone have any ideas for troubleshooting?
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