fix manual bedscript section

Author: pyrevo

docs/.ipynb_checkpoints/bedscript-checkpoint.ipynb

@@ -4,12 +4,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Convert DMCs table to BED format\n",
+    "# Convert the DMCs table to BED format\n",
     "This section describes how to convert the DMCs table to standard BED format using the ChAMP2bed.py script.\n",
     "\n",
     "\n",
     "## Method\n",
-    "Python3 must be installed on your system, no additional libraries required. If your system lacks any python installation please refer to this page: [Python 3 Installation & Setup Guide](https://realpython.com/installing-python/).\n",
+    "Python3 must be installed on your system, no additional libraries are required. If your system lacks any python installation, please refer to this page: [Python 3 Installation & Setup Guide](https://realpython.com/installing-python/).\n",
     "\n",
     "### Description\n",
     "To use ChAMP2bed.py open a terminal and move to the directory storing your main *methylR* results. ChAMP2bed.py must be in the same directory storing your DMCs table:\n",
@@ -22,11 +22,11 @@
     "python3 ChAMP2bed.py myDMC_EPIC_BatchCorrected.txt\n",
     "```\n",
     "\n",
-    "Or adjust with the actual filename for your table. It will produce a new file with the same filename from your table but with .bed extension:\n",
+    "Or adjust with the actual filename for your table. It will produce a new file with the same filename from your table but with the *.bed* extension:\n",
     "\n",
     "![dir](images/bed3.png)\n",
     "\n",
-    "You can use this file as input for Gviz or import either in IGV or as a custom track in any other genome browser. Be sure to match the proper genome version used to perform the analysis and to download the correct GTF/GFF3 file if you want to display the CpG (blue) together with additional features, such as genes (green):\n",
+    "You can use this file as input for Gviz or import it either in IGV or as a custom track in any other genome browser. Be sure to match the proper genome version used to perform the analysis and to download the correct GTF/GFF3 file if you want to display the CpG (blue) together with additional features, such as genes (green):\n",
     "\n",
     "![dir](images/bed4.png)"
    ]

docs/bedscript.ipynb

@@ -4,12 +4,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Convert DMCs table to BED format\n",
+    "# Convert the DMCs table to BED format\n",
     "This section describes how to convert the DMCs table to standard BED format using the ChAMP2bed.py script.\n",
     "\n",
     "\n",
     "## Method\n",
-    "Python3 must be installed on your system, no additional libraries required. If your system lacks any python installation please refer to this page: [Python 3 Installation & Setup Guide](https://realpython.com/installing-python/).\n",
+    "Python3 must be installed on your system, no additional libraries are required. If your system lacks any python installation, please refer to this page: [Python 3 Installation & Setup Guide](https://realpython.com/installing-python/).\n",
     "\n",
     "### Description\n",
     "To use ChAMP2bed.py open a terminal and move to the directory storing your main *methylR* results. ChAMP2bed.py must be in the same directory storing your DMCs table:\n",
@@ -22,11 +22,11 @@
     "python3 ChAMP2bed.py myDMC_EPIC_BatchCorrected.txt\n",
     "```\n",
     "\n",
-    "Or adjust with the actual filename for your table. It will produce a new file with the same filename from your table but with .bed extension:\n",
+    "Or adjust with the actual filename for your table. It will produce a new file with the same filename from your table but with the *.bed* extension:\n",
     "\n",
     "![dir](images/bed3.png)\n",
     "\n",
-    "You can use this file as input for Gviz or import either in IGV or as a custom track in any other genome browser. Be sure to match the proper genome version used to perform the analysis and to download the correct GTF/GFF3 file if you want to display the CpG (blue) together with additional features, such as genes (green):\n",
+    "You can use this file as input for Gviz or import it either in IGV or as a custom track in any other genome browser. Be sure to match the proper genome version used to perform the analysis and to download the correct GTF/GFF3 file if you want to display the CpG (blue) together with additional features, such as genes (green):\n",
     "\n",
     "![dir](images/bed4.png)"
    ]