I am trying to do a meta-analysis with 9 different studies. However, when I pass the closed reference OTU picking when SILVA and Grean Gene, I am losing 4 studies by the time I get to the core-metrics, using 1000 sequences per sample.
I think all of the reads from the samples from the 4 studies are not recognized by the closed reference sequences, resulting in no reads in any samples from the 4 missing studies.
Is this normal? Is there another way around this problem?