Update docs/BIOI611_analysis_10x_dataset_PBMC.ipynb

Bix4UMD · Nov 14, 2024 · 372f8b7 · 372f8b7
1 parent 722582b
commit 372f8b7
Showing 1 changed file with 21 additions and 42 deletions.
diff --git a/docs/BIOI611_analysis_10x_dataset_PBMC.ipynb b/docs/BIOI611_analysis_10x_dataset_PBMC.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "7361b872",
+   "id": "c96ee930",
    "metadata": {},
    "source": [
     "# \n",
@@ -13,7 +13,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c4fa7fad",
+   "id": "9e1c1300",
    "metadata": {},
    "source": [
     "You can download the data from the link [here](https://www.10xgenomics.com/datasets/5k-human-pbmcs-3-v3-1-chromium-controller-3-1-standard)\n",
@@ -30,7 +30,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "bc62b984",
+   "id": "e6ea4674",
    "metadata": {},
    "outputs": [
     {
@@ -51,7 +51,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d768fb8e",
+   "id": "3b30c93a",
    "metadata": {},
    "source": [
     "### Check R1 and R2"
@@ -64,7 +64,7 @@
     }
    },
    "cell_type": "markdown",
-   "id": "93ced0e1",
+   "id": "1b5c476e",
    "metadata": {},
    "source": [
     "\n",
@@ -93,7 +93,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "1b9347d3",
+   "id": "d2e85177",
    "metadata": {},
    "outputs": [
     {
@@ -123,7 +123,7 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "id": "844e16f8",
+   "id": "4ab5c886",
    "metadata": {},
    "outputs": [
     {
@@ -152,15 +152,15 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5114bfd7",
+   "id": "5266ae52",
    "metadata": {},
    "source": [
     "## Run Cellranger \n"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "25fe6349",
+   "id": "c80f9234",
    "metadata": {},
    "source": [
     "Cell Ranger is a software suite developed by 10x Genomics for processing and analyzing data from their single-cell RNA-seq (scRNA-seq), single-cell ATAC-seq (scATAC-seq), and other single-cell assays. Cell Ranger performs tasks such as alignment, filtering, UMI counting, and data aggregation, streamlining the analysis of single-cell datasets generated by 10x Genomics platforms.\n",
@@ -180,7 +180,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "accac6bc",
+   "id": "5ac4ad96",
    "metadata": {},
    "outputs": [
     {
@@ -199,7 +199,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "id": "51f9add6",
+   "id": "ddad1985",
    "metadata": {},
    "outputs": [
     {
@@ -241,7 +241,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f95c5fba",
+   "id": "37b0c514",
    "metadata": {},
    "source": [
     "Input files/folder for `cellranger count`:\n",
@@ -257,7 +257,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "e50a0d91",
+   "id": "b49dc793",
    "metadata": {},
    "outputs": [
     {
@@ -317,15 +317,15 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f498c3e5",
+   "id": "a6e3487e",
    "metadata": {},
    "source": [
     "### Output folder"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "e7d25d36",
+   "id": "3b606516",
    "metadata": {},
    "source": [
     "The job you submitted will generate an output folder: \n"
@@ -334,7 +334,7 @@
   {
    "cell_type": "code",
    "execution_count": 12,
-   "id": "2bcc20e3",
+   "id": "ea269dd2",
    "metadata": {},
    "outputs": [
     {
@@ -391,7 +391,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a7e24143",
+   "id": "ebc16d22",
    "metadata": {},
    "source": [
     "You can also find a copy here:\n",
@@ -403,7 +403,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8dbc5def",
+   "id": "b6b674ef",
    "metadata": {},
    "source": [
     "The summary file in html format is the first file you will check:\n",
@@ -419,7 +419,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2bdd8c5a",
+   "id": "64cdc3c3",
    "metadata": {},
    "source": [
     "The three files below are usually used as input for downstream analysis. "
@@ -428,7 +428,7 @@
   {
    "cell_type": "code",
    "execution_count": 14,
-   "id": "4133bfb6",
+   "id": "9cafe997",
    "metadata": {},
    "outputs": [
     {
@@ -448,7 +448,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "073a544c",
+   "id": "6830e79c",
    "metadata": {},
    "source": [
     "The folder above contains only detected cell-associated\n",
@@ -461,27 +461,6 @@
     "dimensionality reduction, normalize gene\n",
     "expression)."
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "d211706c",
-   "metadata": {},
-   "source": [
-    "## Reference\n",
-    "\n",
-    "https://teichlab.github.io/scg_lib_structs/methods_html/10xChromium3.html\n",
-    "\n",
-    "https://bioinformatics.ccr.cancer.gov/docs/getting-started-with-scrna-seq/2024-04-17_KimiaDadkhah.pdf\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6da687e3",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {