Hi @Nicholas_Bokulich and @KMaki,
Sorry for my delayed response - thank you both very much for your input!
This makes sense - @cjone228 and I are completely new to bioinformatics so we are learning along the way. It didn't occur to us until last week that we were importing mixed reads using SingleEndFastqManifestPhred33V2. We now see on the Qiime2 Docs importing data page that "In this variant of the fastq manifest format, the read directions must all either be forward or reverse."
I think that it makes sense for us to re-orient our reads as @Jen_S did because approximately half of our reads are F and half R.
@KMaki, your reply post on VSEARCH is very clear (thank you!) - however I think @cjone228 and I need to take a step back and work on re-doing the initial steps before we get to this point.
@Nicholas_Bokulich, I would be happy to contribute to a tutorial, however I need to figure out what I am doing first!
Now I have a few new discoveries / questions that go back to late February when I was going through output files from Ion Reporter with @colinbrislawn:
It occurred to me that I only listed a few of the files that IR spits out. Turns out it also spits out the following list:
I see that IR is using Qiime v 1.9.1, so is it possible for me to convert some of these files into Qiime2 compatible files and use them? My concern is that IR does everything through it's own server, so we wouldn't have access to any of the intermediate files (if there are any). Also, I am happy to open more of the folders and show you what is in them if that is helpful.
I see that I have some taxonomy .biom files, so yesterday I was trying to convert the OTU_family.biom file into a Qiime2 .qza file. I found this post and attempted to follow the instructions (see screenshot below)
I picked --type FeatureData [Taxonomy] because is doesn't look like my file has any sequences in it and I picked --input-format BIOMV210Format because my file states "BIOM-Format 2.1.7" and it was made with Qiime v 1.9.1 (see .biom contents in screenshot below)
As always, if anyone has any insight I greatly appreciate it!