OTU filtering thresholds for soil ITS metabarcoding – none of my tested filters seem appropriate
Hi,
I am working on soil ITS metabarcoding data using the FROGS pipeline and I am struggling to choose an appropriate filtering threshold for my OTUs. I have tested two approaches (relative abundance filtering with various thresholds, including 0.00005 as recommended in the literature, and filtering by removal of singletons (inf2) / doubletons (inf3) / etc.), but the abundance curves I obtain (number of OTUs vs. number of reads) do not seem satisfactory in either case.
I am attaching both figures to illustrate.
What do you think? Is there an issue with my data? Am I going about this the wrong way?
Thanks in advance for your advice!
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