update phase docs

open2c · Mar 26, 2024 · fc282e4 · fc282e4
1 parent ffbde6b
commit fc282e4
Showing 1 changed file with 3 additions and 4 deletions.
diff --git a/doc/examples/pairtools_phase_walkthrough.ipynb b/doc/examples/pairtools_phase_walkthrough.ipynb
@@ -7,8 +7,6 @@
    "source": [
     "# Pairtools phase walkthrough\n",
     "\n",
-    "## Pairtools Phase Walkthrough\n",
-    "\n",
     "Welcome to the pairtools phase walkthrough! This notebook will guide you through the process of resolving contacts between homologous chromosomes using haplotype-resolved Hi-C analysis.\n",
     "\n",
     "## What is haplotype-resolved Hi-C?\n",
@@ -111,7 +109,7 @@
    "id": "5ab026af-fe25-4a70-82ef-52af6fb25371",
    "metadata": {},
    "source": [
-    "## Create the reference genome\n",
+    "## Create the homolog-resolved genome\n",
     "\n",
     "To phase input reads, we need to map the data to the concatenated genome with two haplotypes. \n",
     "Below, we will generate such genome in several steps. You will need a reference genome, and one or two lists of mutations to instroduce to the reference.\n",
@@ -588,7 +586,8 @@
    "id": "a8a9fd19",
    "metadata": {},
    "source": [
-    "# Map data with bwa mem to diploid genome\n",
+    "## Map data with bwa mem to diploid genome\n",
+    "\n",
     "In homolog-resolved Hi-C experiments, reads are first aligned against the reference genome and then parsed with pairtools, similar to the standard pairtools-based Hi-C pipeline. However, an additional challenge arises in distinguishing between un-phaseable reads (reads that map equally well to two homologous locations on two homologous chromosomes) and multimappers (reads that map to repeats in the genome).\n",
     "\n",
     "To differentiate between these cases, we can examine the top three candidate alignments for each read:\n",