add extra exercise

docs/comparing-metagenomes.md

@@ -121,19 +121,46 @@ If you plot this via MDS, you'll see a clear separation:
 Points to discuss:
 
 * what does this all mean, in ~microbial terms? Hint: ask Mani to
-  revist how the test data sets were generated!
+  revist how the test data sets were generated! Alternatively,
+  go on to the next section!
+
+## Extra: examining taxonomy
 
-<!--
+If we quickly run our [taxonomy analysis](single-metagenomes-taxonomy.md) on
+one of the other samples, we can maybe start to see some of the reasons for
+the differences in diversity but not richness:
 
-## Comparing based on taxonomy
+```
+mamba activate tax
 
+sourmash scripts fastgather ../data/tutorial_other/CD240.sig.zip \
+    ../databases/gtdb-rs214-k31.zip -o CD240.x.gtdb-rs214.fastgather.csv -c 16
 
+sourmash gather ../data/tutorial_other/CD240.sig.zip \
+    ../databases/gtdb-rs214-k31.zip -o CD240.x.gtdb-rs214.gather.csv \
+    --picklist CD240.x.gtdb-rs214.fastgather.csv:match_name:ident
+    
+sourmash tax metagenome -g CD240.x.gtdb-rs214.gather.csv \
+    -t ../single-metag/gtdb-rs214.lineages.sqldb -F human
 ```
-mamba create -y -n workshop-r r-base r-tidyverse r-vegan r-ape r-rcolorbrewer
 
+You should see:
 ```
+sample name    proportion   cANI   lineage
+-----------    ----------   ----   -------
+CD240             42.2%     94.0%  d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides uniformis
+CD240             19.5%     94.5%  d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides fragilis
+CD240             12.6%     94.1%  d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides distasonis
+CD240             11.7%     91.2%  d__Bacteria;p__Bacillota_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B
+CD240             11.4%     -      unclassified
+CD240              2.6%     91.4%  d__Bacteria;p__Bacillota_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_D
+```
+
+That's right - both samples have similar species, but the abundances of those
+species are quite different.
 
--->
+Note that in this case that's not an accident: the dataset was created
+specifically to contain only five species ;).
 
 ---