Update docs/BIOI611_long_read_transcriptome.ipynb

Bix4UMD · Nov 9, 2024 · a2c4d74 · a2c4d74
1 parent 035e773
commit a2c4d74
Showing 1 changed file with 25 additions and 6 deletions.
diff --git a/docs/BIOI611_long_read_transcriptome.ipynb b/docs/BIOI611_long_read_transcriptome.ipynb
@@ -5,7 +5,8 @@
     "colab": {
       "provenance": [],
       "toc_visible": true,
-      "authorship_tag": "ABX9TyNQDb5F5pRzJqqOjEJ9xIRf"
+      "authorship_tag": "ABX9TyOP4Qg/QFS49fm8w+o7D7m0",
+      "include_colab_link": true
     },
     "kernelspec": {
       "name": "python3",
@@ -16,6 +17,16 @@
     }
   },
   "cells": [
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "view-in-github",
+        "colab_type": "text"
+      },
+      "source": [
+        "<a href=\"https://colab.research.google.com/github/Bix4UMD/BIOI611_lab/blob/main/docs/BIOI611_long_read_transcriptome.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
+      ]
+    },
     {
       "cell_type": "markdown",
       "source": [
@@ -80,7 +91,7 @@
     {
       "cell_type": "markdown",
       "source": [
-        "## Run `wf-transcriptome` on the demo datasets\n",
+        "### Run `wf-transcriptome` on the demo datasets\n",
         "\n",
         "The workflow `wf-transcriptome` has a demo datasets. This demo datasets can be used to test the workflow and help you undestand the input and output.\n",
         "\n",
@@ -152,10 +163,18 @@
         "| JSON configuration file for IGV browser | igv.json | JSON configuration file to be loaded in IGV for visualising alignments against the reference. | aggregated |\n",
         "| BAM file (minimap2) | BAMS/{{ alias }}.reads_aln_sorted.bam | BAM file generated from mapping input reads to the reference. | per-sample |\n",
         "| BAM index file (minimap2) | BAMS/{{ alias }}.reads_aln_sort.bam.bai | Index file generated from mapping input reads to the reference. | per-sample |\n",
+        "\n"
+      ],
+      "metadata": {
+        "id": "XiZX7duip6s2"
+      }
+    },
+    {
+      "cell_type": "markdown",
+      "source": [
+        "### Run `wf-transcriptome` on the direct RNA sequencing data from C. elegans\n",
         "\n",
-        "## Run `wf-transcriptome` on the direct RNA sequencing data from C. elegans\n",
-        "\n",
-        "Based on the demo data, you can set up the input folder and run the workflow using the job file:\n",
+        "Based on the demo data, you can set up the input folder and run the workflow on the direct RNA from the Genome Research paper.\n",
         "\n",
         "```\n",
         "# Takes around 14 minutes to finish\n",
@@ -169,7 +188,7 @@
         "```\n"
       ],
       "metadata": {
-        "id": "XiZX7duip6s2"
+        "id": "byU91iQvKC9T"
       }
     },
     {