Orienting Reads with classifier-consensus-vsearch

[SoilRotifer (Mike Robeson)]

Hi @Nicolette_HernandezK,

If you search the forum you'll find several posts, like the ones below about reorienting reads using RESCRIPt:

Discarded results produced by q2-cutadapt's trim-paired when working with mixed-orientation reads

Summary We recently discovered a bug related to the q2-cutadapt plugin's demux-paired command that, in certain situations, can unnecessarily discard a significant portion of reads, when the command is run with the --p-mixed-orientation flag. Impact This issue impacts the following versions of q2-cutadapt: 2020.6 2020.8 If you think you may have been impacted please check your provenance at https://view.qiime2.org for the versions listed above to verify that you ran demux-paired with the mixe…

Rescript Plugin for 18S

Hi @lmjackson, welcome to :qiime2:! Can you provide details on which primer set you used to generate your sequence data? Many primer sets will amplify off-target sequences. That is just the nature of the process. How much of your sequence data is being returned as Bacterial? Few? Many? I would advise against removing removing groups of taxa just because your are unable to identify what you want. In fact, it is best to leave these "outgroup" taxa within your database. This way you can more c…

-Cheers!