I need to merge the feature table.qza and rep-seqs.qza for single end sequences and paired-end sequences. Any possibilites to perform? Because for meta-analysis, I have both paired and single end sequences. If the table.qza to be merged, further process like OTU, diversity analysis will be performed.
How to perform this?
Thanks in advance.
Thanks for reaching out, that's a great question!
You can definitely perform analysis on both of these data types - here's what I recommend:
Analyze each set of reads (paired vs. single end) separately and then merge after denoising. If your read lengths differ by a lot, you could use an OTU clustering approach after denoising to cluster the denoised reads together.
I'd recommend using dada2 for your denoising method, since you are using both forward and reverse reads (with your paired end dataset).
Details on OTU clustering can be found here, if you do end up needing to go that route.
Hope this helps!