Sorry if this is repeated question.
I have 2x Miseq runs of identical samples that I am in the process of analysing. From what I have read the best thing to do is denoise the samples separately then merge them after confirming the results between the 2 runs are not significantly different.
Assuming they aren’t, what is the best way to merge the 2 lots of data? I have read about group and merge-tables but I’m not sure which is best for me.
And at what stage should I merge the runs? As in should I merge the feature tables then perform taxonomic classification on the combined table?