Good morning ,
I am seeking clarification on the appearance of singletons in my feature table after using the core-metrics-phylogenetic pipeline.
I am working with a feature table prepared from two sequencing runs(Run A & Run B). Each run was performed with same sequencing protocol but at different facilities. After denoising each run with DADA2 there are two singletons present in feature table from Run A and none in the feature table from Run B. Based on posts on the forum, I understand these can be introduced during the merging of forward and reverse reads.
After merging the individual denoised data with qiime feature-table merge, the resulting feature table contains ~ 11,809 ASVs (n = 68 samples at this point). However, after running this table through qiime diversity core-metrics-phylogenetic (–p-sampling-depth 10000), the rarefied table (n = 66 samples) contains 11,138 ASVs, of which ~ 900 are singletons.
I don’t quite understand how these singletons appear in the feature table and would appreciate any insight.
A quarantined qiime-er.