Practical-6-MAG-analyses.md

@@ -2,7 +2,14 @@
 
 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, go to your marmic2021 environment and get checkm:
+First, remove the old environment (that has the wrong version of python):
+
+```
+$ conda remove --py27 --all
+
+```
+
+then load your marmic2021 environment and get checkm:
 
 ```
 $ conda install -c bioconda checkm-genome