Practical-6-MAG-analyses.md

 # Bin statistics
 
 Now that we have a couple of bins, let's do some basic statistics and compare: genome length, N50, and number of contigs. How bins compare between technologies? do you see any big differences in terms of statistic metrics? For instance, try to come up with a comparison of Illumina vs PacBio bins. Use a couple and check if you see big differences between technologies.
+
+If you were not able to get bins, check the following folders in the result directory:
+
+```
+$ day_4/01.Illumina/03.binning
+$ day_4/02.PacBio/03.binning
+```
 | ILMN or PACB bin | Number of contigs | N50 | genome length |
 |------------------|-------------------|-----|---------------|
 | ILMN |  |  |  |
@@ -18,7 +25,13 @@ $ checkm lineage_wf -f checkm_MaxBin.txt --tab_table -x fasta -t 10 --pplacer_th
 
 **Like we mentioned above, we have previously run checkM for all bins .** Find the bins and result of checkM in today's folder. From this point forward, we will be referring to this last group of bins.
 
-See the output file generated by checkM (<span dir="">out_checkM_marmic2021-allbins.tab</span>). It should look something like this:
+See the output file generated by checkM:
+
+```
+$ day_4/03.checkM/out_checkM_marmic2021-allbins.tab
+```
+
+It should look something like this:
 
 ```plaintext
 Bin Id  Marker lineage  # genomes       # markers       # marker sets   0       1       2       3       4       5+      Completeness    Contamination   Strain heterogeneity