Metagenomics Tutorial (Older) answers

These are the answers to the questions from the older 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:

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: