I know that you do not advise to remove the singletons, but I would like to test the pipeline with and without removing the singletons. Thus, I am not sure about the sub.sample script. I am following more or less the MiSeqs SOP. Thus, the scripts that I am doing are: … pre.cluster -> chimera.uchime -> remove.seqs -> summary.seqs -> pcr.seqs ->
classify.seqs -> remove.lineage -> count.groups -> sub.sample -> rename.file -> cluster.split -> cluster.split -> make.shared -> filter.shared -> sub.sample -> summary.single…
I am not sure whether or not to maintain the first “sub.sample” after the “count.groups” in the pipeline?
Thanks in advance!