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Bix4UMD · Sep 16, 2024 · 350c889 · 350c889
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diff --git a/docs/bulkRNAseq_lab.ipynb b/docs/bulkRNAseq_lab.ipynb
@@ -189,15 +189,15 @@
   },
   {
    "cell_type": "markdown",
-   "id": "302aaf00",
+   "id": "3f1c8a42",
    "metadata": {},
    "source": [
     "## Download raw fastq files"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "80708d91",
+   "id": "d85fdda7",
    "metadata": {},
    "source": [
     "```\n",
@@ -214,19 +214,59 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4b73f096",
+   "id": "e574da47",
    "metadata": {},
    "source": [
     "## Quality control "
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "c2849452",
+   "id": "c9298b90",
    "metadata": {},
    "source": [
-    "FASTQC -> CTrim Galore -> FASTQC "
+    "1. Use FastQC to check the quality of fastq files:"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6951d0e5",
+   "metadata": {},
+   "source": [
+    "```\n",
+    "%%bash\n",
+    "cd /scratch/zt1/project/bioi611/user/$USER\n",
+    "sbatch ../../shared/scripts/bulkRNA_s1_fastqc.sub\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3a223f5a",
+   "metadata": {},
+   "source": [
+    "2. Use `trim galore` to remove adaptors, low quality bases and low quality reads. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2f673a41",
+   "metadata": {},
+   "source": [
+    "```\n",
+    "%%bash\n",
+    "cd /scratch/zt1/project/bioi611/user/$USER\n",
+    "sbatch ../../shared/scripts/bulkRNA_s2_trim_galore.sub\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "84fb878c",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

diff --git a/docs/s1_lab_RNAseq_lab.ipynb b/docs/s1_lab_RNAseq_lab.ipynb