I have around 1004 samples (16s) which are downloaded for the ENA website. These samples are sequenced using Ion Torrent. Is it advisable to denoise using DADA2 separately (maybe 100 sequences at a time) and use merge-seqs to merge it or denoise all the samples at a time.? Will there be any changes…?
DADA2’s error model construction assumes it is working with a single sequencing run, so your best bet is probably to split your samples by sequencing run, and denoise each run independently of the others. Merging after DADA2 is recommended.
There’s been a lot of great discussion about IonTorrent workflows here, and I’d recommend you do some searching . This topic is a good place to start.
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