I sequenced numerous amplicon-seq libraries today and found the sequence per tile quality to be highly variable across the fastq files. I initially thought I had overclustered or debris was present upon/within the flow cell but a third of the fastq files look good. I have clustered the same library type previously at 1200K and never had this issue. My run metrics were pretty good:
~1000M cluster density, 85% PF, 91%>Q30
Any help would be greatly appreciated.
Can I even use this data for downstream analysis?
Collection of FastQC images below:
~1000M cluster density, 85% PF, 91%>Q30
Any help would be greatly appreciated.
Can I even use this data for downstream analysis?
Collection of FastQC images below:
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