fix #10

materials/10-phylogenetics.md

@@ -272,8 +272,9 @@ iqtree \
 ```
 
 - We extract the variant sites and count of invariant sites using `SNP-sites`.
-- We specify as input the `aligned_pseudogenomes_masked_snps.fas` produced in the previous step of the script by running `SNP-sites`.
-- We specify the number of constant sites, also generated from the previous exercise. We can use `$(cat results/snp-sites/constant_sites.txt)` to directly add the contents of `constant_sites.txt` without having to open the file to obtain these numbers.
+- As input to both `snp-sites` steps, we use the `aligned_pseudogenomes_masked_snps.fas` produced in the previous step of our analysis.
+- The input alignment used in `iqtree` is the one from the previous step. 
+- The number of constant sites was specified in the script as `$(cat results/snp-sites/constant_sites.txt)`. This allows to directly add the contents of the `constant_sites.txt` file, without having to open the file to obtain these numbers.
 - We use as prefix for our output files "Nam_TB" (since we are using the "Namibian TB" data), so all the output file names will be named as such.
 - We automatically detect the number of threads/CPUs for parallel computation.
 - We specify the maximum amount of memory and threads/CPUs to use for computation.

materials/23-panaroo.md

@@ -182,18 +182,6 @@ combined_protein_cdhit_out.txt.clstr  gene_presence_absence.Rtab
 core_alignment_filtered_header.embl   gene_presence_absence.csv
 ```
 
-The script included other code - which we didn't need to fix - that extracted the variable sites from our alignment (as detailed in [Building phylogenetic trees](10-phylogenetics.md)). These steps took as input the alignment file generated by Panaroo:
-
-```bash
-# extract variable sites
-snp-sites results/panaroo/core_gene_alignment.aln > results/snp-sites/core_gene_alignment_snps.aln
-
-# count invariant sites
-snp-sites -C results/panaroo/core_gene_alignment.aln > results/snp-sites/constant_sites.txt
-```
-
-These two steps of the analysis produce the two files that we want to use in the next exercise.
-
 :::
 :::
 
@@ -210,10 +198,9 @@ Produce a tree from the core genome alignment from the previous step.
 - Run the script using `bash scripts/03-run_iqtree.sh`. Several messages will be printed on the screen while `IQ-TREE` runs. 
 
 :::{.callout-hint}
-For IQ-TREE: 
+For _SNP-sites_: 
 
-- The constant sites can be obtained by looking at the output of the `snp-sites` in `results/snp-sites/constant_sites.txt` (or in the `preprocessed` folder if you are still waiting for your `Panaroo` analysis to finish).
-- The input alignment should be the output from the `snp-sites` program in `results/snp-sites/core_gene_alignment_snps.aln` (or in the `preprocessed` folder if you are still waiting for your `Panaroo` analysis to finish).
+- The input alignment should be the output from the `panaroo` program found in `results/panaroo/` (or in the `preprocessed` folder if you are still waiting for your analysis to finish).
 
 :::
 
@@ -227,6 +214,12 @@ The fixed script is:
 # create output directory
 mkdir -p results/iqtree/
 
+# extract variable sites
+snp-sites results/panaroo/core_gene_alignment_filtered.aln > results/snp-sites/core_gene_alignment_snps.aln
+
+# count invariant sites
+snp-sites -C results/panaroo/core_gene_alignment_filtered.aln > results/snp-sites/constant_sites.txt
+
 # Run iqtree
 iqtree \
   -fconst $(cat results/snp-sites/constant_sites.txt) \
@@ -239,8 +232,9 @@ iqtree \
   -bb 1000
 ```
 
-- We specify as input the `core_gene_alignment_snps.aln` produced in the previous exercise by running `Panaroo` followed by `SNP-sites`.
-- We specify the number of constant sites, also generated from the previous exercise. We can use `$(cat results/snp-sites/constant_sites.txt)` to directly add the contents of `constant_sites.txt` without having to open the file to obtain these numbers.
+- We extract the variant sites and count of invariant sites using `SNP-sites`.
+- As input to both `snp-sites` steps, we use the `core_gene_alignment_snps.aln` alignment produced by _Panaroo_ in the previous step of our analysis.
+- The number of constant sites was specified with `$(cat results/snp-sites/constant_sites.txt)` to directly add the contents of the `constant_sites.txt` file, without having to open the file to obtain these numbers.
 - We use as prefix for our output files "School_Staph" (since we are using the data from the schools Staph paper), so all the output file names will be named as such.
 - We automatically detect the number of threads/CPUs for parallel computation.
 

materials/28-recombination.md

@@ -150,6 +150,12 @@ Now that we have created a recombination-masked alignment, we can extract the va
 - Fix the script provided in `scripts/04-run_iqtree.sh`. See @sec-iqtree if you need a hint of how to fix the code in the script.
 - Run the script using `bash scripts/04-run_iqtree.sh`. Several messages will be printed on the screen while `IQ-TREE` runs. 
 
+:::{.callout-hint}
+For _SNP-sites_: 
+
+- The input alignment should be the output from the `gubbins` program found in `results/gubbins/` (or in the `preprocessed` folder if you are still waiting for your analysis to finish).
+:::
+
 :::{.callout-answer}
 
 The fixed script is: 
@@ -180,7 +186,8 @@ iqtree \
   -bb 1000
 ```
 
-- The script starts by extracting variable sites using _SNP-sites_. We used as input the `aligned_pseudogenomes_masked_snps.fas` file produced in the previous exercise.
+- We extract the variant sites and count of invariant sites using `SNP-sites`.
+- As input to both `snp-sites` steps, we use the `aligned_pseudogenomes_masked_snps.fas` file produced in the previous exercise.
 - The next step runs _IQ-tree_:
   - We specify the number of constant sites, also generated from the previous exercise. We can use `$(cat results/snp-sites/constant_sites.txt)` to directly add the contents of `constant_sites.txt` without having to open the file to obtain these numbers.
   - We use as prefix for our output files "sero1" (since we are using the data from the Chaguza serotype 1 paper), so all the output file names will be named as such.