I have collected data that includes both V3-V4 and V4 region amplicons, some of which have already been paired-end merged. After merging all the data, can I analyze them together in QIIME2?
Hello @zhenchen361,
Welcome to the forums!
Many of the programs made for amplicon analysis assume that all reads are from the exact same region. So the answer is...
Maybe?
See this long discussion about working with multiple regions: Possible Analysis Pipeline for Ion Torrent 16S Metagenomics Kit Data in QIIME2?
That was 4 years ago, and while we have some better options now, it's not easy.
If I had a data set like this, I would try to trim everything to a common region (like V4) to avoid this challenge.
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