diff --git a/scrna/scarches_scvi_tools.ipynb b/scrna/scarches_scvi_tools.ipynb
index 2d20f57..7e2669a 100644
--- a/scrna/scarches_scvi_tools.ipynb
+++ b/scrna/scarches_scvi_tools.ipynb
@@ -297,9 +297,15 @@
     "id": "2C37BM-pCM_o"
    },
    "source": [
-    "We train the reference using the standard SCVI workflow, except we add a few non-default parameters that were identified to work well with scArches."
+    "We train the reference using the standard SCVI workflow, except we add a few non-default parameters that were identified to work well with scArches. \n",
+    "It is essential to encode covariates here as this allows scArches to map new batches in the encoder to the existing data and thereby provides batch integration. "
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": 11,