Strange pattern to dada2 output

Technical Support
3

Hello Jeff,

Welcome to the forums! :qiime2:

That is an extremely strange run for many small reasons.

  • Illumina's new binned quality scores: discussed here
  • Very even reads-per-sample
    Min of 13k and max of 22k is fantastic! How did you get that to happen?
  • Blocks of sample losing 99% of reads during the quality filter

That last one is the big mystery! :male_detective:

A sequencing core at a previous employer had a strange issue like this.
We discovered a problem with the liquid-handling robot we used to do PCR. :robot:

I recommend lateral thinking. :brain:
Can you check the PCR plate layout?
Were these stored in a different freezer, run in a different thermocycler?
What primers did you use?

1 Like