First Time Qiime-er needing guidance

[colinbrislawn (Colin J Brislawn)]

Hello @Hayley_Guay,

I think you are off to a very good start! I can confirm that your imported data looks OK, and you should be ready to proceed with the next steps show in the various tutorials. On to dada2!

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@Hayley_Guay

Any tips for choosing parameters for trimming/truncating based on my data?

Try this thread: Merging, Quality control and overlapping

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@Hayley_Guay

Looking ahead, should I use --p-pooling-method Independent or Pseudo? Any resources for the difference here that is more in-depth than the docstring on the QiimeDocs page?

Try the original DADA2 docs! Pseudopooling is discussed in vivid detail on this page: Increasing the sensitivity of DADA2 with prior information

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@Hayley_Guay

Any egregious errors in this process so far?

Not that I can see!

@Hayley_Guay

Like I said, I am relatively inexperienced with this analysis, so I'd appreciate any suggestions or resources anyone can think to offer. My experiment set-up is a bit different than what the tutorials offer, which makes me want to be extra careful with each step to make sure my data is valid.

I think you are doing exceptionally well, especially given that you are working with ITS data, which can be tricky. Let us know if you have any more questions along the way. :qiime2: