splitt musicc

R/Analyze_genecatalog.Rmd

@@ -386,10 +386,6 @@ hist(shannon_diversity)
 
 Normalize gene counts to **gene counts per million**, which is analogous to transcripts per million.
 
-Alternative ways to normalize would be to normalize to single copy genes. 
-Example the one from [MuSiCC](https://github.com/borenstein-lab/MUSiCC/blob/master/musicc/data/uscg_76_kegg_min_2313.lst)
-
-MUSiCC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome. Ohad Manor and Elhanan Borenstein. Genome Biology
 
 ```{r }
 
@@ -509,6 +505,15 @@ heatmap(log_annoation_cpm,
 
 
 
+## Alternative ways to normalize
+
+An other interesting way to normalize would be to normalize to single copy genes. 
+Example the one from [MuSiCC](https://github.com/borenstein-lab/MUSiCC/blob/master/musicc/data/uscg_76_kegg_min_2313.lst)
+
+MUSiCC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome. Ohad Manor and Elhanan Borenstein. Genome Biology
+
+
+
 ## Integrate them in a SummarizedExperiment object
 
 ```{r }