Practical-6-MAG-analyses.md

@@ -2,7 +2,7 @@
 
 One way of checking the quality of your bins is to look at the presence/absence/duplication of single-copy marker genes in the respective bins. There are several sets of single-copy marker genes used by different programs. Today we will show you an example using the program checkM. A nice feature of checkM is that in addition to the estimation of completeness and contamination it will place your bins in a reference phylogenomic tree. From that, you will directly get information about the approximate taxonomic classification of your bins. Unfortunately, checkM is not easy to install but it is almost installed in the servers. We need to add a bit more files to make it work first. We first need to download the database to a local folder. MAKE SURE you are in a folder with enough space for the database and for a bunch of files that we will be generating.<br>
 
-First, let's download the database from the source:
+~~First, let's download the database from the source:
 ```
 $ wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
 
@@ -17,9 +17,11 @@ Next create a python 2.7 environment:
 After the files are unpacked, you need to tell checkM that you have the database available:
 
 ```
-$ checkm data setRoot <database location>
+$ checkm data setRoot <database location>~~
 ```
 
+***
+
 If everything went well you should be able to run checkM on your generated bins using a command like the one below. Please select no more than 20 MAGs so you don't have to wait forever.
 
 ```