Update docs/BIOI611_scRNA_seq_cele_cellranger.ipynb

Bix4UMD · Dec 2, 2024 · 2aa880c · 2aa880c
1 parent d8ccdb5
commit 2aa880c
Showing 1 changed file with 4 additions and 31 deletions.
diff --git a/docs/BIOI611_scRNA_seq_cele_cellranger.ipynb b/docs/BIOI611_scRNA_seq_cele_cellranger.ipynb
@@ -4,7 +4,7 @@
   "metadata": {
     "colab": {
       "provenance": [],
-      "authorship_tag": "ABX9TyMFyELCr+oxSe7wC6yZYhmf",
+      "authorship_tag": "ABX9TyMnBOK1zaB4XJp605WWiYHL",
       "include_colab_link": true
     },
     "kernelspec": {
@@ -26,15 +26,6 @@
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@@ -49,17 +40,19 @@
         "/scratch/zt1/project/bioi611/shared/raw_data/10x_cele_data/scRNA/\n",
         "\n",
         "\n",
+        "\n",
         "1.   If you want to download and prepare the files yourself,\n",
         "\n",
         "\n",
         "\n",
-        "here is the process:\n",
+        "Here is the process:\n",
         "\n",
         "For each sample, fetch the sra files using `prefectch`\n",
         "\n",
         "For example:\n",
         "\n",
         "```\n",
+        "export PATH=/scratch/zt1/project/bioi611/shared/software/sratoolkit.3.1.1-centos_linux64/bin:$PATH\n",
         "prefetch SRR8611967\n",
         "```\n",
         "\n",
@@ -167,26 +160,6 @@
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 }