Titlecase

openpaul · Aug 31, 2024 · 6b323cd · 6b323cd
1 parent 35f9587
commit 6b323cd
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/_posts/2024-06-02-Lieberman-Aiden.ipynb b/_posts/2024-06-02-Lieberman-Aiden.ipynb
@@ -35,7 +35,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## The paper\n",
+    "## The Paper\n",
     "\n",
     "The paper describing Hi-C for the first time is Lieberman-Aiden et al. (2009):\n",
     "\n",
@@ -51,7 +51,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Getting set up\n",
+    "## Getting Set Up\n",
     "\n",
     "First things first, let's find the data and setup a python environment. \n",
     "I am using mamba for this, but you can choose any way to organize your code. \n",
@@ -79,7 +79,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Getting the data\n",
+    "### Getting the Data\n",
     "\n",
     "The authors write that the plot 1B was produced using the cell line GM and the restriction enzyme HindIII. The NGS dataset is said to have 8.4 million reads and 6.7 valid interactions. Unfortunately they do not write down which sample id corresponds to that. \n",
     "\n",
@@ -147,7 +147,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Alignment\n",
+    "## Making Alignments\n",
     "To align the reads, one first needs to index the reference genome.\n",
     "I make an index for BWA and for Minimap2, so I can use both of them later when needed.\n",
     "\n",
@@ -180,7 +180,7 @@
     "\n",
     "I will align the data using those two approaches and in addition I will be using Minimap2's default to see if that makes a difference at all.\n",
     "\n",
-    "### Alignment using BWA and custom settings\n",
+    "### Alignment using BWA and Custom Settings\n",
     "\n",
     "For BWA I use as many threads as I can get my hands on, in my case that's 12. I am also using the flags `-5SP`. \n",
     "The `SP` flag will skip any mate rescue, as far as I understand this means that it will not try to move the paired-read \n",
@@ -212,7 +212,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Alignment of reads separately\n",
+    "### Alignment of Reads Separately\n",
     "\n",
     "For this approach I simply treat both the forward and the reverse read as separate datasets. To avoid Minimap2 automatically recovering any connection between the two, I am performing two separate alignments. This way I am sure the aligner does what I think it does. \n",
     "\n",