removed zipcodes

Author: joannmudge

module_notebooks/06-read-mapping-with-vg.ipynb

@@ -186,9 +186,9 @@
     "\n",
     "The parameters:  \n",
     "\n",
+    "`-p`  show progress  \n",
     "`-Z`  .gbz file  \n",
     "`-m`  .min file  \n",
-    "`-z`  zipcode file  \n",
     "`-d`  .dist file  \n",
     "`-f`  fastq file (use more than once if feeding in paired-end read files)\n",
     "\n",
@@ -201,7 +201,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!vg giraffe -Z graphs/yprp.chrVIII.pggb.giraffe.gbz -m graphs/yprp.chrVIII.pggb.shortread.withzip.min -z graphs/yprp.chrVIII.pggb.shortread.zipcodes -d graphs/yprp.chrVIII.pggb.dist -f reads/SK1.illumina_1.fastq.gz -f reads/SK1.illumina_2.fastq.gz > alignments/SK1xyprp.chrVIII.pggb.mapped.gam"
+    "!vg giraffe -p -Z graphs/yprp.chrVIII.pggb.giraffe.gbz -m graphs/yprp.chrVIII.pggb.min -d graphs/yprp.chrVIII.pggb.dist -f reads/SK1.illumina_1.fastq.gz -f reads/SK1.illumina_2.fastq.gz > alignments/SK1xyprp.chrVIII.pggb.mapped.gam"
    ]
   },
   {
@@ -240,11 +240,11 @@
     "<details>\n",
     "<summary>Click for help</summary>\n",
     "<br>\n",
-    "!vg giraffe -Z graphs/yprp.fullgenome.pggb.giraffe.gbz -m graphs/yprp.fullgenome.pggb.shortread.withzip.min -z graphs/yprp.fullgenome.pggb.shortread.zipcodes -d graphs/yprp.fullgenome.pggb.dist -f reads/SK1.illumina_1.fastq.gz -f reads/SK1.illumina_2.fastq.gz > alignments/SK1xyprp.fullgenome.pggb.mapped.gam  \n",
+    "!vg giraffe -Z graphs/yprp.fullgenome.pggb.giraffe.gbz -m graphs/yprp.fullgenome.pggb.min -d graphs/yprp.fullgenome.pggb.dist -f reads/SK1.illumina_1.fastq.gz -f reads/SK1.illumina_2.fastq.gz > alignments/SK1xyprp.fullgenome.pggb.mapped.gam  \n",
     "\n",
     "<br><br>\n",
     "\n",
-    "!vg giraffe -Z graphs/yprp.allchrs.pggb.giraffe.gbz -m graphs/yprp.allchrs.pggb.shortread.withzip.min -z graphs/yprp.allchrs.pggb.shortread.zipcodes -d graphs/yprp.allchrs.pggb.dist -f reads/SK1.illumina_1.fastq.gz -f reads/SK1.illumina_2.fastq.gz > alignments/SK1xyprp.allchrs.pggb.mapped.gam\n",
+    "!vg giraffe -Z graphs/yprp.allchrs.pggb.giraffe.gbz -m graphs/yprp.allchrs.pggb.min -d graphs/yprp.allchrs.pggb.dist -f reads/SK1.illumina_1.fastq.gz -f reads/SK1.illumina_2.fastq.gz > alignments/SK1xyprp.allchrs.pggb.mapped.gam\n",
     "</details>"
    ]
   },
@@ -511,6 +511,12 @@
   }
  ],
  "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",