Hello there. I am running the merge-pairs function for deblur and I would like to confirm as to what counts as a "successful" merge. I'm aware of the verbose function as well as the two qza files (merged and unmerged). So far, these two don't bring up any red flags.
My main concern is the visualization from here:
euk-merged-filtered.qzv (328.3 KB)
I can see the obvious spot where the forward and reverse reads merge towards the middle. I wasn't able to find information from the forum (though perhaps I didn't look hard enough) about what counts as a successful merging; is it supposed to have this ladder effect in the middle?
Hi @ricknematodeguy
This is expected for per-merged data like you have.
In this diagram, we can see really good quality on your forward read (the first step of the ladder), the increased quality and condifience you get from merging the reads in the middle (the second step), and the slightly worse quality of the reverse read (the last step). This is kinda creating a ladder effect but there is nothing that stands out to me as wrong.
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