Update 1.5.2_Viral_Taxonomy_and_Phylogeny_II.md

Author: vmkhot

_episodes/1.5.2_Viral_Taxonomy_and_Phylogeny_II.md

@@ -208,7 +208,7 @@ We've built two python scripts using this library to shrink the size of tree out
 
 > ## Exercise - Post-process your tree
 >
-> Use the below sbatch script make your tree and post-process it. You will have change the contig name in the sbatch script. **Note:** See exercise question #10 below - you might want to plot this 'pet contig' here, or the one from yesterday!
+> Use the below sbatch script make your tree and post-process it. You will have change the contig name in the sbatch script. **Note:** See exercise question #4 below - you might want to plot this 'pet contig' here, or the one from yesterday!
 >
 > Please pause once you have made the trees! We will visualize the tree together with a demo in itol **so that you can make nice graphics to include in your lab books**! 
 >
@@ -262,14 +262,13 @@ We've built two python scripts using this library to shrink the size of tree out
 >{: .source}
 {: .solution}
 
-### vConTACT3 
+## vConTACT3 
 
 vConTACT3 has an underlying assumption that the fraction of shared genes between two viruses represents their evolutionary relationship. The vConTACT3 gene-sharing network closely correlates with the ICTV taxonomy. 
 
 > ## Exercise - run vConTACT3
 > 
-> {:start='6'}
-> 6. Run vcontact3 on your virome dataset
+> Run vcontact3 on your virome dataset
 >
 > You will need the following commands for the conda environment and database
 > 
@@ -301,7 +300,6 @@ vConTACT3 has an underlying assumption that the fraction of shared genes between
 >{: .source}
 {: .challenge}
 
-
 > ## sbatch script to run vcontact3
 > ```bash
 >#!/bin/bash
@@ -341,25 +339,26 @@ vConTACT3 has an underlying assumption that the fraction of shared genes between
 > 
 > ### General Questions
 > 
->{:start='7'}
->7. What percentage of your total viral contigs were classified by vConTACT3?
->8. How can you judge the accuracy of your taxonomic classifications?
->9. What is the maximum taxonomic distance between viruses that are still connected in the vConTACT3 graph?
+>{:start='1'}
+>1. What percentage of your total viral contigs were classified by vConTACT3?
+>2. How can you judge the accuracy of your taxonomic classifications?
+>3. What is the maximum taxonomic distance between viruses that are still connected in the vConTACT3 graph?
 >
 > **Pick one pet viral contig that has a terL gene and also a taxonomic classification by vConTACT3**
 >
->{:start='10'} 
->10. What is the taxonomy classifcation of your *pet contig* from vConTACT3 and the terL tree?
->11. How many genes are shared with known reference viruses? *(vConTACT3 results)*
->12. If your classifications are/were different between the terL tree and the vConTACT3 - which classification would you trust more?
+>{:start='4'} 
+>4. What is the taxonomy classifcation of your *pet contig* from vConTACT3 and the terL tree?
+>5. How many genes are shared with known reference viruses? *(vConTACT3 results)*
+>6. If your classifications are/were different between the terL tree and the vConTACT3 - which classification would you trust more?
 >
-> ### Optional/Group Discussions
+> ### Group Discussions
+> 
+>{:start='7'}
+>7. Explore the cytoscape network visualization and/or terL tree together - include a graphic of at least 1 tree
+>8. What do long branches on your terL tree mean?
+>9. What does a rooted versus an unrooted tree represent?
+>10. What are the limitations of using the terL tree? and could you overcome these limitations?
 > 
->{:start='12'}
->13. Explore the cytoscape network visualization and/or terL tree together
->14. What do long branches on your terL tree mean?
->15. Where are the contigs assigned to long branches in the network from vConTACT3? 
->16. What are the limitations of using the terL tree? and could you overcome these limitations?
 > {: .source}
 {: .challenge}