fixed file names

ncgr · Feb 6, 2025 · 125b157 · 125b157
1 parent c59c6f2
commit 125b157
Showing 1 changed file with 28 additions and 4 deletions.
diff --git a/module_notebooks/04-read-mapping-with-vg.ipynb b/module_notebooks/04-read-mapping-with-vg.ipynb
@@ -178,8 +178,8 @@
     "<div class=\"alert alert-block alert-info\"> <b>Try this:</b>  \n",
     "    <ul>\n",
     "        <li>Create a blank code cell below.</li>\n",
-    "        <li>Align the SK1 reads to the graph created directly from the full genome (yprp.fullgenome.pggb.xg).</li>\n",
-    "        <li>Align the SK1 reads to the graph created by combining the 16 chromosomal subgraphs (yprp.allchrs.pggb.vg).</li>\n",
+    "        <li>Align the SK1 reads to the graph created directly from the full genome (yprp.fullgenome.pggb.giraffe.gbz).</li>\n",
+    "        <li>Align the SK1 reads to the graph created by combining the 16 chromosomal subgraphs (yprp.allchrs.pggb.giraff.gbz).</li>\n",
     "    </ul>"
    ]
   },
@@ -190,7 +190,7 @@
     "<details>\n",
     "<summary>Click for help</summary>\n",
     "<br>\n",
-    "!vg giraffe -p -Z yprp.fullgenome.pggb.giraffe.gbz -m yprp.fullgenome.pggb.min -d yprp.fullgenome.pggb.dist -f SK1.illumina_1.fastq.gz -f SK1.illumina_2.fastq.gz > SK1xyprp.fullgenome.pggb.mapped.gam\n",
+    "!vg giraffe -p -Z yprp.fullgenome.pggb.giraffe.gbz -m yprp.fullgenome.pggb.min -d yprp.fullgenome.pggb.dist -f SK1.illumina_1.fastq.gz -f SK1.illumina_2.fastq.gz > SK1xyprp.fullgenome.pggb.mapped.gam  \n",
     "<br>\n",
     "!vg giraffe -p -Z yprp.allchrs.pggb.giraffe.gbz -m yprp.allchrs.pggb.min -d yprp.allchrs.pggb.dist -f SK1.illumina_1.fastq.gz -f SK1.illumina_2.fastq.gz > SK1xyprp.allchrs.pggb.mapped.gam\n",
     "</details>"
@@ -368,7 +368,31 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "environment": {
+   "kernel": "conda-env-nigms-pangenomics-nigms-pangenomics",
+   "name": "workbench-notebooks.m127",
+   "type": "gcloud",
+   "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m127"
+  },
+  "kernelspec": {
+   "display_name": "nigms-pangenomics",
+   "language": "python",
+   "name": "conda-env-nigms-pangenomics-nigms-pangenomics"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.8"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 4
 }