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Metagenomics Tutorial Answers (HUMAnN1)

Gavin Douglas edited this page Oct 5, 2017 · 1 revision

These are the answers to the questions from the Metagenomics Tutorial.

Introduction and taxonomic section:

  1. 30

  2. 10

  3. 60,000/sample

  4. MetaPhlAn version 2.5.0 (28 April 2015)

  5. s__Neisseria_unclassified 11.8%

  6. SRS015044: p__Actinobacteria & SRS015893: p_Firmicutes

  7. Phylum Candidatus_Saccharibacteria, present only in sample SRS015044

  8. Sample SRS015044 was from supragingival plaque

  9. metaphlan_out

  10. Yes, there is separation between the tongue samples and the plaque samples but there is no clear separation between subgingival and supragingival. The separation occurs mainly along PCs 1 and 2:

  11. You should see this plot:

boxplot_answer

Functional section:

  1. SRS015893
  2. No
  3. 50 (KOs different across body sites)
  4. 2 (KEGG Pathways different across body sites)
  5. ko00281: Geraniol degradation . corrected p-value: 4.14e-4
  6. 5
  7. Higher in the tongue samples.
  8. Should look like this:
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