I am having trouble understanding the steps of analyzing my cDNA samples.
So, the sequenced data that I have is single, and it’s based on multiple regions, v3, v4, v67, v8, v9…
So I have multiple primers that are used in the sequencing process.
When I do analysis, here is what I did:
importing the files,
cutting the primers using cutadapt
denoising using dada2
generating taxonomic table using green genes.
generating bar plot.
The thing that’s confusing me is the following:
when I cut the primers, do I cut ALL the 5 primers from the all the samples and carry on with the analysis?
do I cut primer v3, carry on the analysis, store the data, then cut primer v4, carry on the analysis, store the data etc… till I cut every primer on its own and do the analysis for each trim I did?
What is the difference from both steps? Because it seems that I am getting different bar plot for the species present when I carry on these different steps.
Also, let’s say I do the second technique I mentioned, would there be a way in qiime2 to merge these results?