Practical-5-Assembly-and-binning.md

@@ -53,13 +53,13 @@ Given the limited time we have during the class, we have previously generated th
 
 The assemblies are located here:
 
-```
+```plaintext
 day_3
 ```
 
 For the generation of the PacBio assemblies we used the following command:
 
-```
+```plaintext
 flye -t 8 --meta  --pacbio-hifi sample.1.fa  -o sample.pacbio
 ```
 
@@ -105,7 +105,9 @@ run_MaxBin.pl -contig Q.contigs.fa -thread 10 -min_contig_length 1500 -abund dep
 
 What did we get as an output from MaxBin? Try to run stats.sh on your bins like we did before for the assembly and see what you think of the output. Think about what we know and what we don’t know about these bins; we’ll talk more in the next session how we can check that we’ve recovered the genomes that were in the original dataset and how we can further investigate them.
 
-**Additional activity for advanced students**
+Now that we have some bins we can move to the next section. If for some reason you were not able to get bins - don't worry! just check the `results/` folder and use the bins we have previously generated.
+
+# **Additional activity for advanced students**
 
 ## Anvi’o