I wan to analyze samples from different projects in one Qiime2 run but I have paired-end ad single-end sequences and I don’t know how to qiime tools import since I have two different type of sequences (PairedEndFastqManifestPhred33 and SingleEndFastqManifestPhred33)
If you have multiple different projects / sequencing runs that you wish to compare, you must import, demultiplex, and denoise separately, then merge, as shown in this tutorial. This is assuming that you plan to use dada2 or deblur for denoising; it is okay to merge earlier if you use OTU picking.
Import separately, as described above.
No matter whether you are using denoising or OTU picking, to perform a proper comparison you will need to analyze the same amplicon site (primers) and same length, and ideally processed in the same way (read joining of any type would violate this). So I recommend that you only use the forward reads from both studies and trim to the same length, i.e., discard the reverse reads from the second study.
I hope that helps!
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