Listed the distances to use in the visualization of the original and augmented graph in 07; made sure Bandage was capitalized for consistency.

Author: joannmudge

module_notebooks/07-variant-calling-with-vg.ipynb

@@ -627,7 +627,7 @@
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-    "2. Then visualize the CUP1 region in bandage for the original graph (yprp.chrVIII.pggb.gfa) and the augmented graph (SK1xyprp.chrVIII.pggb.aug.gfa).\n",
+    "2. Then visualize the CUP1 region in Bandage for the original graph (yprp.chrVIII.pggb.gfa) and the augmented graph (SK1xyprp.chrVIII.pggb.aug.gfa). In Bandage, under graph drawing, 100 is a good distance to use for the original graph and 200 for the augmented graphs. These distances will ensure that you extend far enough out from the BLAST hits so that the region is fully connected.\n",
     "\n",
     "<div class=\"alert alert-block alert-info\"> <b>NOTE:</b> The augmented graph is much bigger and it will have difficulty loading the entire chrVIII graph. So, before drawing the graph, BLAST the genes, then change the \"Scope\" to \"Around query hits,\" and change \"Distance\" to 200 for the augmented graph. Finally, click \"Draw Graph\" to apply these changes.</div>\n"
    ]