So I have 2 projects that has been done. One sequencing project is group A (@6samples) which is sequenced with Ion Torrent S5 so I see that the result only have one fq.gz for every sample as the raw data (single end). The other project is sequencing group B and C (@6samples, total 12 samples) with Illumina Novaseq so the result has two fq.gz as the raw data (pair end) for every sample. For both project I already have the clean tags (.fna files) for every sample and even the OTU .biom files
Now I want to compare between the 3 groups.
But I notice that I cannot just merely start by merging both the OTU .biom files because they both have the same OTU_ID but with different taxonomy (like both have OTU_1 but with different taxonomy details).
So I’m trying to start with by concatenating all the .fna files from every sample (total 18 files) into one file and start with clustering sequences with q2-vsearch tutorial with open reference clustering with 16s database from SILVA.
And then I notice this From QIIME fna to QIIME2 diversity and taxonomy data and see that I can’t actually just concatenating all the .fna files together because it will result in a mess (?)
And from that forum, he recommends the user to start from the raw files… But I’m confused now since the raw files I had is different types, one group is single end while the other two is pair end…
So… any idea on how to start analysing this 3 groups…? Thank you so much for your help sorry I’ve been trying to find the similar topic but I can’t find it