I have two samples as both dada2 and deblur failed, I opted for vsearch in order to get feature table as table.qza and feature sequences as rep-seq.qza. I operated both samples individually.
For one sample, I tried to cluster the sequences at 99% getting rep-seqs-dn-99.qza.
The size of the rep-seqs.qza is 2.2 GB and of rep-seqs-dn-99.qza is 794.1 Mb.
I have been running qiime2 fragment insertion as an alternative as mafft failed to process more than million sequences.
But it has been almost two weeks that it is running using rep-seqs.qza using 60 threads, and yesterday only I started operating the same on rep-seqs-dn-99.qza.
My questions are
Is it okay to process samples independently as I do not have metadata file and my ultimate aim is diversity analysis?
I do not know whether to work on rep-seqs.qza or rep-seqs-dn-99.qza?
What is the next step after clustering otus at 99
How to get the otu network map from this information?
If for example, I want to see the relationship of one OTU with other using Pearson correlation, is it possible and how?
I have been struggling with this since past one month for now, please help me at the earliest.
Should I stop because fragment insertion step as it is taking a lot of time and no other work am I able to do because of the server being occupied.
Thank you very much