Split apart blocks and added some text.

module_notebooks/07-visualization.ipynb

@@ -52,9 +52,13 @@
     "\n",
     "Pangenomic graphs can be very complex, often looking like \"hairballs\". Bandage allows us to zoom in on interesting regions to visualize and interact with them.\n",
     "\n",
-    "![Compressed de Bruijn graphs “hairballs”: https://academic.oup.com/bioinformatics/article/30/24/3476/2422268](./Figures/hairballsB.png)\n",
-    "\n",
-    "\n",
+    "![Compressed de Bruijn graphs “hairballs”: https://academic.oup.com/bioinformatics/article/30/24/3476/2422268](./Figures/hairballsB.png)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "#### Graphical Fragment Assembly (GFA) format\n",
     "\n",
     "Bandage uses the Graphical Fragment Asembly (GFA) format.\n",
@@ -63,8 +67,13 @@
     "+ Originally developed for representing genomes during assembly\n",
     "+ Now used for pangenomics\n",
     "\n",
-    "More information on GFA format is available [here:](https://github.com/GFA-spec/GFA-spec).\n",
-    "\n",
+    "More information on GFA format is available [here:](https://github.com/GFA-spec/GFA-spec).\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "#### Bandage\n",
     "\n",
     "Bandage is an interactive graph visualizer. The Bandage acronym stands for:\n",
@@ -80,10 +89,16 @@
     "\n",
     "Bandage also allows you to label and color nodes by uploading comma separated value (CSV) text files with metadata.\n",
     "\n",
-    "Details on creating CSV files can be found [here:](https://github.com/rrwick/Bandage/wiki/CSV-labels).\n",
-    "\n",
+    "Details on creating CSV files can be found [here:](https://github.com/rrwick/Bandage/wiki/CSV-labels).\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "##### Example graph\n",
     "\n",
-    "##### **Group exercise:**{-}\n",
+    "XXX in progress\n",
     "\n",
     "1. Copy the following example graph from inbre to your computer:\n",
     "```\n",
@@ -94,8 +109,13 @@
     "4. If your have BLAST, find [CUP1](https://www.yeastgenome.org/locus/S000001095) and [YHR054C](https://www.yeastgenome.org/locus/S000001096) via BLAST\n",
     "  + How many copies are in the graph?\n",
     "  + What does the structure it’s in look like?\n",
-    "  + Take a screenshot of the region that CUP1 is in with the gene colored\n",
-    "\n",
+    "  + Take a screenshot of the region that CUP1 is in with the gene colored\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "#### General Feature Format (GFF)\n",
     "\n",
     "https://genome.ucsc.edu/FAQ/FAQformat.html#format3"