What happens if you spike-in more PhiX than you thought? I had a good Read1 (Q30 of 87%) but very high PhiX alignment (60%) and very low Q30 in read 2 (only 39%). Is this caused by over clustering? Clustering density 800 with a V3 2x300
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Cluster density up to 1400 is within v3 specification (https://www.illumina.com/systems/seq...fications.html) and Illumina's specifciation is based on PhiX library sequencing. Low Q30 value for R2 must have some other reasons and best to contact the Tech support for diagnosis.
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