Begin RGP analyses tutorial

labgem · Nov 23, 2023 · dde306c · dde306c
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diff --git a/docs/index.md b/docs/index.md
@@ -53,6 +53,7 @@ Those RGPs can be further divided in conserved modules by panModule ([Bazin et a
 tutorial/prepEnv
 tutorial/inputData
 tutorial/workflows
+tutorial/AnalyseRGP
 ```
 
 ```{toctree}

diff --git a/docs/tutorial/AnalyseRGP.md b/docs/tutorial/AnalyseRGP.md
@@ -0,0 +1,17 @@
+# Region of genomic plasticity prediction
+## Predict the region of genomic plasticity from the partitioned pangenome graph
+
+"Regions of genome plasticity (**RGPs**) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to genomic islands (GIs)." [Bazin et al. 2020](https://doi.org/10.1093/bioinformatics/btaa792)
+
+We are going to start from the partitioned pangenome graph build in the [previous step](#build-and-partition-a-pangenome-graph). 
+
+You can predict the RGP with PPanGGOLiN with this command:
+
+```
+ppanggolin rgp -p B_janonicum_results/pangenome.h5
+```
+
+As explain before, PPanGGOLiN will predict and store the RGPs in the pangenome file. Follow the 
+
+## Analyse RGPs predicted by PPanGGOLiN
+### Get the list of RGPs predicted by PPanGGOLiN