Hey you all!
I’m a PhD Student that is trying to figure out how to analyze Ion Torrent Data. I think I already have my final pipeline described, almost all of it. However, I need to answer one last question to myself and I think your advice could be really helpful.
The main doubt I am facing is that I don’t know whether to trim my sequences or maintain their lengths. As a first approach, I did the trun-len as it is explained in the QIIME2 tutorials, therefore, trimming the sequences when the Quality Score gets down. However, when I came across the post where a IonTorrent Data Pipeline is described, I read the following comment:
Could you clarify? Are you using extract-reads on the reference sequences? If so, don’t use
trunc-len on those reads (since your query seqs are in mixed orientations they can hit at either end of that read)
Did this mean to not trunc-len Ion Torrent Data in general?
Another question I have is if it is necessary to do a Closed-Reference OTU clustering (as it was described in that previous post) or if It is possible to work directly with the ASV created in DADA2 step.
Thank you so much in advanced! I’m a bit lost and I will appreciate your help