QIIME2 - sample integrity and database related questions

General Discussion
1

Hello everyone,

I had the following questions that I would love to hear people's thoughts on:

  1. In the FeatureTable, if a sample shows a decreased frequency of features (or OTUs), does that mean the sample integrity has been compromised or sample may have been degraded during the initial sequencing steps?
  2. As I performed the steps of the "moving pictures" tutorial, I learned that there was only the Greengenes database that was used for the taxonomic profiling. Is there a way to choose a database of our liking while carrying out the QIIME pipeline?

I look forward to hearing from the community.

Thank you in advance,
Aakarsha.

2

An off-topic reply has been merged into an existing topic: QIIME2 - database, sample integrity, cutoff scores

Please keep replies on-topic in the future.