combination different dataset

[SoilRotifer (Mike Robeson)]

Hi @Rm733,

If each run was processed identically with the same primers, then you can merge your feature-tables, sequences and taxonomy files. Here is an example from the Fecal microbiota transplant tutorial.

If these data were produced via different primer sets, you can use closed-reference OTU picking. More details are here:

Combining studies from same 16S region but with different primers

Hi @azan, welcome to !, For the case in which you have data from amplicon region, but with different primer pairs, there are a few options you can try below. Note: regardless of the approach you use, you'll still have to worry about slight variations in PCR / sequencing biases in your results. Which may inflate differences between data sets. It only takes a single base in a primer to alter what you observe in your data. Alter the trim & truncation settings for each run, using these s…