why are my 16S data dominated by eukaryotes?

General Discussion
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Hi Chris
I have got low read sequencing. I am using 16s microbiome Miseq Illumina. And the reasuts looks like Eukaryote is dominate and few bacteria.
Do you think getting low read beacaues something wrong happened in amplification during doing PCR or during analysis using qiime2!!
Any suggestions please?

Thank you very much
Samia

2

Hi there @Samia!

This is a huge question! So many ways and places for this to happen. I guess my first suggestion is to look at your sequencing run report, and compare that to the demux summary results in QIIME 2, to ensure you started off soundly. From there, we would need to know more about how you generated you FeatureTable[Frequency] - q2-dada2? q2-deblur? OTU clustering?

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How can be more confidence that my work is good in pcr using 16sbecause sometimes I am thinking that when I got low read that could something happen wrong in pcr however, I have done 4 plates so plate 1&4 working very week but 2&3 not very well ?
Thank you very much
Samia

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