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Data Visualization

  1. Based on the plots you see in demux.qzv, what values would you choose for –p-trunc-len and –p-trim-left in this case?
  2. View the table.qzv QIIME 2 artifact, and in particular the Interactive Sample Detail tab in that visualization. What value would you choose to pass for –p-sampling-depth? How many samples will be excluded from your analysis based on this choice? How many total sequences will you be analyzing in the core-metrics-phylogenetic command?
  3. Which categorical sample metadata columns are most strongly associated with the differences in microbial community richness? Are these differences statistically significant?
  4. Which categorical sample metadata columns are most strongly associated with the differences in microbial community evenness? Are these differences statistically significant?
  5. Are the associations between subjects and differences in microbial composition statistically significant? How about body sites? What specific pairs of body sites are significantly different from each other?
  6. Do the Emperor plots support the other beta diversity analyses we’ve performed here? (Hint: Experiment with coloring points by different metadata.)
  7. What differences do you observe between the unweighted UniFrac and Bray-Curtis PCoA plots?
  8. When grouping samples by “body-site” and viewing the alpha rarefaction plot for the “observed_features” metric, which body sites (if any) appear to exhibit sufficient diversity coverage (i.e., their rarefaction curves level off)? How many sequence variants appear to be present in those body sites?
  9. When grouping samples by “body-site” and viewing the alpha rarefaction plot for the “observed_features” metric, the line for the “right palm” samples appears to level out at about 40, but then jumps to about 140. What do you think is happening here? (Hint: be sure to look at both the top and bottom plots.)
  10. Recall that our rep-seqs.qzv visualization allows you to easily BLAST the sequence associated with each feature against the NCBI nt database. Using that visualization and the taxonomy.qzv visualization created here, compare the taxonomic assignments with the taxonomy of the best BLAST hit for a few features. How similar are the assignments? If they’re dissimilar, at what taxonomic level do they begin to differ (e.g., species, genus, family, …)?
  11. Visualize the samples at Level 2 (which corresponds to the phylum level in this analysis), and then sort the samples by body-site, then by subject, and then by days-since-experiment-start. What are the dominant phyla in each in body-site? Do you observe any consistent change across the two subjects between days-since-experiment-start 0 and the later timepoints?
  12. Which sequence variants differ in abundance across Subject? In which subject is each sequence variant more abundant? What are the taxonomies of some of these sequence variants? (To answer the last question you’ll need to refer to another visualization that was generated in this tutorial.)
  13. Which genera differ in abundance across subject? In which subject is each genus more abundant?

Sample Solution

Feng shui is an old Chinese rationality about how people and their surroundings cooperate and have connections. It incorporates the rule that everything has vitality and is associated with everything else. It is stemmed in the conviction that dependent on laws of nature, standards, hypotheses and methods we can see how to make a situation that enables us to be in amicability and parity. It additionally can control us to improve certain parts of our lives. The fundamental rule of feng shui is chi or vitality. It is a feng shui rule that is utilized through all of life. It interfaces the vitality of everything together. There can be chi or vitality of earth, the air and individuals. We can see the nature of chi communicated through regions of shading, frame, shape, sound and the different cycles in nature. Feng shui standards work to guarantee that the chi is permitted to continue streaming and not stall out or exhausted. In feng shui standards, there are two primary kinds of feng shui that we have to consider. One of these is physical and contains the genuine structures, environment, structures, streets and plan. Alternate includes directional impacts that in spite of the fact that are imperceptible, still have an effect on our lives and how we identify with existence. We have to take both feng shui standards into thought while assessing the chi characteristics of a domain. As indicated by feng shui, if a zone in the earth isn't being helpful for giving great chi, there are fixes or settles that we can use to restore the chi to a characteristic solid state and keep on streaming all through the space. We can settle or address the feng shui of a region by making little or enormous alterations and applying feng shui procedures. These strategies fuse the utilization of various components to make equalization and concordance.

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