I had a Metagenomic 16s rRNA run on MiSeq v3 kit 2 x300 cycles. with good PF >89% but low quality q30 <40%. Kindly advice what could get wrong?

I had a metagenomic run on MiSeq using v3 kits of 16s rRNA v3-v4 region. I have loaded 8pM pooled library with 10% PhiX spike-in. MiSeq run had 89% PF with 16 M raw reads but with very low q30...

14 April 2018 5,784 11 View