I have two MiSeq runs that have to be pre-processed and demultiplexed in QIIME 1 prior to importing into QIIME 2. These runs have overlapping barcodes. I want to run these two datasets together through clustering with the Open Reference VSearch tool.
What is the best way to combine these runs and still retain the sample IDs? I see two options: 1) Should I CAT the seq.fna file outputs from QIIME 1 and then import this new merged file into QIIME 2?
I run dereplication and chimera filtering in QIIME 2 prior to VSearch - so
2) is there a way to merge these filtered .qza sequence and table files prior to clustering in QIIME 2? This second option allows me to filter out PCR errors and sequencing artifacts from each individual run and seems to me to be the more accurate way to process my two runs prior to merging but I am uncertain on how to merge the two sets of .qza files after this point but before I do the OTU picking step.
Thank you very much,