├── .gitignore ├── Capstone ├── Akondy-etal-2016.pdf ├── Capstone-Rubric.pdf ├── Ichikawa-etal-2019.pdf ├── Sergestolpe-etal-2016.pdf ├── Xin-etal-2016.pdf └── Xin-etal-2016_NCM.csv ├── Configuration.md ├── Homework ├── .DS_Store ├── HW1-Key_Bash-Basics.ipynb ├── HW2-Key_Scripting+Jobs_Bash.ipynb ├── HW3-Key_Introduction-to-R.ipynb ├── HW4-Key_Data-Analysis+Plotting_R.ipynb ├── HW5-Key_Advanced-Plotting+RNA-Seq_R.ipynb ├── data │ ├── .DS_Store │ ├── NAV-D14_DEseq2.csv │ ├── RNASeq_post-processing.csv │ ├── art │ │ └── artists.txt │ ├── fastq │ │ ├── simulated1.R1.fq │ │ ├── simulated1.R2.fq │ │ ├── simulated2.R1.fq │ │ ├── simulated2.R2.fq │ │ ├── simulated3.R1.fq │ │ ├── simulated3.R2.fq │ │ ├── simulated4.R1.fq │ │ ├── simulated4.R2.fq │ │ ├── simulated5.R1.fq │ │ └── simulated5.R2.fq │ ├── games.csv │ └── tmp │ │ ├── file1.txt │ │ ├── file10.txt │ │ ├── file100.txt │ │ ├── file101.txt │ │ ├── file102.txt │ │ ├── file103.txt │ │ ├── file104.txt │ │ ├── file105.txt │ │ ├── file106.txt │ │ ├── file107.txt │ │ ├── file108.txt │ │ ├── file109.txt │ │ ├── file11.txt │ │ ├── file110.txt │ │ ├── file111.txt │ │ ├── file114.txt │ │ ├── file115.txt │ │ ├── file116.txt │ │ ├── file117.txt │ │ ├── file118.txt │ │ ├── file119.txt │ │ ├── file12.txt │ │ ├── file120.txt │ │ ├── file121.txt │ │ ├── file122.txt │ │ ├── file123.txt │ │ ├── file124.txt │ │ ├── file125.txt │ │ ├── file126.txt │ │ ├── file127.txt │ │ ├── file128.txt │ │ ├── file129.txt │ │ ├── file13.txt │ │ ├── file130.txt │ │ ├── file131.txt │ │ ├── file132.txt │ │ ├── file133.txt │ │ ├── file134.txt │ │ ├── file135.txt │ │ ├── file136.txt │ │ ├── file138.txt │ │ ├── file139.txt │ │ ├── file14.txt │ │ ├── file140.txt │ │ ├── file141.txt │ │ ├── file142.txt │ │ ├── file143.txt │ │ ├── file144.txt │ │ ├── file145.txt │ │ ├── file146.txt │ │ ├── file147.txt │ │ ├── file148.txt │ │ ├── file149.txt │ │ ├── file15.txt │ │ ├── file150.txt │ │ ├── file151.txt │ │ ├── file152.txt │ │ ├── file153.txt │ │ ├── file154.txt │ │ ├── file155.txt │ │ ├── file156.txt │ │ ├── file157.txt │ │ ├── file158.txt │ │ ├── file159.txt │ │ ├── file16.txt │ │ ├── file160.txt │ │ ├── file161.txt │ │ ├── file162.txt │ │ ├── file163.txt │ │ ├── file164.txt │ │ ├── file165.txt │ │ ├── file166.txt │ │ ├── file167.txt │ │ ├── file168.txt │ │ ├── file169.txt │ │ ├── file17.txt │ │ ├── file170.txt │ │ ├── file171.txt │ │ ├── file172.txt │ │ ├── file173.txt │ │ ├── file174.txt │ │ ├── file175.txt │ │ ├── file176.txt │ │ ├── file177.txt │ │ ├── file178.txt │ │ ├── file179.txt │ │ ├── file18.txt │ │ ├── file180.txt │ │ ├── file181.txt │ │ ├── file182.txt │ │ ├── file183.txt │ │ ├── file184.txt │ │ ├── file185.txt │ │ ├── file186.txt │ │ ├── file187.txt │ │ ├── file188.txt │ │ ├── file189.txt │ │ ├── file19.txt │ │ ├── file190.txt │ │ ├── file191.txt │ │ ├── file192.csv │ │ ├── file192.txt │ │ ├── file193.txt │ │ ├── file194.txt │ │ ├── file195.txt │ │ ├── file196.txt │ │ ├── file197.txt │ │ ├── file198.txt │ │ ├── file199.txt │ │ ├── file2.txt │ │ ├── file200.txt │ │ ├── file21.txt │ │ ├── file22.txt │ │ ├── file23.txt │ │ ├── file24.txt │ │ ├── file25.txt │ │ ├── file26.txt │ │ ├── file27.txt │ │ ├── file28.txt │ │ ├── file29.txt │ │ ├── file3.txt │ │ ├── file30.txt │ │ ├── file31.txt │ │ ├── file32.txt │ │ ├── file33.csv │ │ ├── file33.txt │ │ ├── file34.txt │ │ ├── file35.txt │ │ ├── file36.txt │ │ ├── file38.txt │ │ ├── file39.txt │ │ ├── file4.txt │ │ ├── file40.txt │ │ ├── file41.txt │ │ ├── file42.txt │ │ ├── file44.txt │ │ ├── file45.txt │ │ ├── file46.txt │ │ ├── file47.txt │ │ ├── file48.txt │ │ ├── file49.txt │ │ ├── file5.txt │ │ ├── file50.txt │ │ ├── file51.txt │ │ ├── file52.txt │ │ ├── file53.txt │ │ ├── file54.txt │ │ ├── file55.txt │ │ ├── file56.txt │ │ ├── file57.txt │ │ ├── file58.txt │ │ ├── file59.txt │ │ ├── file6.txt │ │ ├── file60.txt │ │ ├── file61.txt │ │ ├── file62.txt │ │ ├── file64.txt │ │ ├── file65.txt │ │ ├── file66.txt │ │ ├── file67.txt │ │ ├── file68.txt │ │ ├── file69.txt │ │ ├── file7.txt │ │ ├── file70.txt │ │ ├── file71.txt │ │ ├── file72.txt │ │ ├── file73.txt │ │ ├── file74.txt │ │ ├── file75.txt │ │ ├── file76.txt │ │ ├── file77.txt │ │ ├── file78.txt │ │ ├── file79.txt │ │ ├── file8.txt │ │ ├── file80.txt │ │ ├── file81.txt │ │ ├── file82.txt │ │ ├── file84.txt │ │ ├── file85.txt │ │ ├── file86.txt │ │ ├── file87.txt │ │ ├── file88.txt │ │ ├── file89.txt │ │ ├── file9.txt │ │ ├── file90.txt │ │ ├── file91.txt │ │ ├── file92.txt │ │ ├── file93.txt │ │ ├── file94.txt │ │ ├── file96.csv │ │ ├── file96.txt │ │ ├── file97.txt │ │ ├── file98.txt │ │ └── file99.txt └── img │ └── kernel_change.png ├── Images └── AB-Issue.png ├── Lectures ├── A1.a_Intro-BashBasics.pptx ├── A1.b_Bash-redirections-pipes.pptx ├── A2.a_Bash-InDepth.pptx ├── A2.b_Bash-loops_scripting.pptx ├── A3.a_R-Intro.pptx ├── A3.b_R-objects-operations.pptx ├── A4.a_R-DataAnalysis.pptx ├── A4.b_R-Plotting.pptx ├── A4_Demos.ipynb ├── B5.a_R-AdvancedPlotting.pptx ├── B5.b_R-DESeq2Figs.pptx ├── B5_Demos.ipynb ├── B6.a_Bash-RNASeq-RawData.pptx ├── B6.a_Demos.ipynb ├── B6.b_Bash-SAMvBAM.pptx ├── B7-Demos.ipynb ├── B7.b_R-ReadCounting.pptx ├── B8-Demo_R.ipynb ├── B8.a_R-Expression-Analysis.pptx ├── B8.b_R-DESeq2Enrichment.pptx ├── B9.a-Data_and_Demo │ ├── R_PCA_solution.ipynb │ └── datasets │ │ ├── 3d_s.csv │ │ ├── Wang_Dapeng_IMMUNITY_2018_simp.csv │ │ ├── Wang_Dapeng_IMMUNITY_2018_simp_colnames.csv │ │ ├── independent_xyz.csv │ │ ├── y_dependent_on_x.csv │ │ └── y_z_dependent_on_x.csv ├── B9.a_R-RNASeq-PCA.pptx ├── B9.b_HPC.pptx ├── C10.a_Capstone-a.pptx ├── C10.b_Capstone-b.pptx ├── C11.a_InvitedTalks-BioinformaticsResearch.pptx └── C11.b_TSRI-BioinformaticsPanel.pptx ├── README.md └── git-installation.md /.gitignore: -------------------------------------------------------------------------------- 1 | **/.ipynb_checkpoints/ 2 | -------------------------------------------------------------------------------- /Capstone/Akondy-etal-2016.pdf: 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The instructions below should work for most recent versions of MacOS, Windows, and Ubuntu. If you do not have a computer with one of those operating systems, or if you have any problems, please contact the course instructurs via the course Slack channel. 3 | 4 | ### Install R 5 | * Follow installation links and instructions at https://cran.rstudio.com/. The current version is R-4.2.1. 6 | * In general, select the installation defaults 7 | * **Windows** 8 | * Select the option for "Install R for the first time" 9 | * If given the option, install RTools4.2. If you forget or do not see the option, install it from [here](https://cran.r-project.org/bin/windows/Rtools/rtools42/rtools.html) (select the "Rtools42 installer"). 10 | * **MacOS** 11 | * Download the file `R-4.2.1.pkg`, then double-click that file. 12 | 13 | ### Install RStudio 14 | * Download the installer for your OS at https://www.rstudio.com/products/rstudio/download/#download 15 | 16 | ### Confirm your installation was successful 17 | * Start RStudio 18 | * Type `plot(1:10)` at the prompt in the "Console" window 19 | * Confirm you see the simple scatter plot in the lower right panel, as shown in the screenshot below 20 | 21 | ![image](https://user-images.githubusercontent.com/2635409/185712070-3cb947e7-ddb0-4d5d-92ea-280ef9a934d1.png) 22 | 23 | 24 | ### RECOMMENDED FOR WINDOWS USERS: Install Windows Subsystem for Linux (WSL) 25 | * Follow instructions in https://docs.microsoft.com/en-us/windows/wsl/install 26 | -------------------------------------------------------------------------------- /Homework/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuLab/Applied-Bioinformatics/7c01300871e64c09fec7ade1af4c2f3c8bb074e5/Homework/.DS_Store -------------------------------------------------------------------------------- /Homework/HW1-Key_Bash-Basics.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": { 6 | "nbgrader": { 7 | "grade": false, 8 | "grade_id": "context_1", 9 | "locked": true, 10 | "schema_version": 3, 11 | "solution": false, 12 | "task": false 13 | } 14 | }, 15 | "source": [ 16 | "# Homework 1: Jupyter and Bash Basics\n", 17 | "Curated by Sabah Ul-Hasan, Karthik Gangavarapu, Shang-Fu Chen, Huitian Dao, and Andrew Su\n", 18 | "\n", 19 | "Complete homework is due every Tuesday at 8 AM PST.
\n", 20 | "Save your homework as you go, so the efforts don't get lost.
\n", 21 | "Note there are up 12 points, but you can only receive 10 points total for homework.\n", 22 | "\n", 23 | "In this assignment, you will
\n", 24 | "A1.aa Practice basic bash operations in terminal and functionality of Jupyter notebook (Python kernel)
\n", 25 | "A1.ab Execute basic operations of bash commands in Jupyter notebook
\n", 26 | "A1.ba Utilize bash for more sophisicated tasks, such as pipes
\n", 27 | "A1.bb Solidfy your understanding of bash by practice\n", 28 | "\n", 29 | "Note that there is a section at the end (A1.bb) to point out any enhancements you personally would make to this assignment if you were to lead the course. " 30 | ] 31 | }, 32 | { 33 | "cell_type": "markdown", 34 | "metadata": { 35 | "nbgrader": { 36 | "grade": false, 37 | "grade_id": "context_2", 38 | "locked": true, 39 | "schema_version": 3, 40 | "solution": false, 41 | "task": false 42 | } 43 | }, 44 | "source": [ 45 | "## A1.aa: Github and Jupyter notebook [20-30 min] Individual\n", 46 | "\n", 47 | "### aa.i Confirmation of Github account and download of data in Bioinformatics course repo " 48 | ] 49 | }, 50 | { 51 | "cell_type": "markdown", 52 | "metadata": { 53 | "nbgrader": { 54 | "grade": false, 55 | "grade_id": "ls_pwd_cd_unzip", 56 | "locked": true, 57 | "points": 0, 58 | "schema_version": 3, 59 | "solution": false, 60 | "task": true 61 | } 62 | }, 63 | "source": [ 64 | "#### Question 1 (1 point)\n", 65 | "- Use command line to find and show where the `data.zip` file is located within `Question1` (using absolute path.)\n", 66 | "- Move it back to `HW1` at the same level with this notebook and then decompress it.\n", 67 | "- Copy out `fastq` folder to `HW1` folder.\n", 68 | "\n", 69 | "Did you find this folder? \n", 70 | "- If yes, show the combination of commands you reach the folder below.\n", 71 | "- If no, type out any obstacles you encounter here.\n", 72 | "\n", 73 | "=== BEGIN MARK SCHEME === \n", 74 | "__Answer:__ \n", 75 | "- Students should use a combination of __`ls`__, __`pwd`__, and __`cd`__ to reach `Question1/here/is/the/answer/data.zip`. \n", 76 | "- Understand and use __`cd ../`__ to return to `HW1` folder.\n", 77 | "- Once there, __`unzip [filename]`__\n", 78 | "- Use __`cp -r`__ to copy the `fastq` folder out.\n", 79 | "\n", 80 | "=== END MARK SCHEME ===" 81 | ] 82 | }, 83 | { 84 | "cell_type": "markdown", 85 | "metadata": { 86 | "nbgrader": { 87 | "grade": true, 88 | "grade_id": "ls_pwd_cd_unzip_answer", 89 | "locked": false, 90 | "points": 1, 91 | "schema_version": 3, 92 | "solution": true, 93 | "task": false 94 | } 95 | }, 96 | "source": [] 97 | }, 98 | { 99 | "cell_type": "markdown", 100 | "metadata": { 101 | "nbgrader": { 102 | "grade": false, 103 | "grade_id": "context_3", 104 | "locked": true, 105 | "schema_version": 3, 106 | "solution": false, 107 | "task": false 108 | } 109 | }, 110 | "source": [ 111 | "\n", 112 | "### aa.ii Confirmation of basic Jupyter notebook operations
\n", 113 | "Use ```jupyter notebook``` to open _HW1_ in your browser. The notebook should be opened in the Notebook Editor as below (for more user interface information, see [the documentation](https://jupyter-notebook.readthedocs.io/en/stable/ui_components.html)):\n", 114 | "\n", 115 | "\n", 116 | "Do you see the same screen as shared by the instructors? (Yes/No)" 117 | ] 118 | }, 119 | { 120 | "cell_type": "markdown", 121 | "metadata": { 122 | "nbgrader": { 123 | "grade": false, 124 | "grade_id": "run_2plus3", 125 | "locked": true, 126 | "schema_version": 3, 127 | "solution": false, 128 | "task": false 129 | } 130 | }, 131 | "source": [ 132 | "#### Question 2 (1 point)\n", 133 | "Run the cell with an output after typing `2+3`.\n", 134 | "\n", 135 | "a. Notice the different settings (ie Markdown). What do they mean?
\n", 136 | "b. Why did we need to install the R kernel, whereas Python 3 was automatically included?
\n", 137 | "c. What additional observations do you have of Jupyter notebook, and how it functions? Play around with it and take notes of your observations. Also, type out any obstacles you encounter here." 138 | ] 139 | }, 140 | { 141 | "cell_type": "code", 142 | "execution_count": 2, 143 | "metadata": { 144 | "nbgrader": { 145 | "grade": true, 146 | "grade_id": "run_2plus3_answer", 147 | "locked": false, 148 | "points": 1, 149 | "schema_version": 3, 150 | "solution": true, 151 | "task": false 152 | } 153 | }, 154 | "outputs": [ 155 | { 156 | "data": { 157 | "text/plain": [ 158 | "5" 159 | ] 160 | }, 161 | "execution_count": 2, 162 | "metadata": {}, 163 | "output_type": "execute_result" 164 | } 165 | ], 166 | "source": [ 167 | "### BEGIN MY SOLUTION\n", 168 | "2+3\n", 169 | "### END MY SOLUTION" 170 | ] 171 | }, 172 | { 173 | "cell_type": "markdown", 174 | "metadata": { 175 | "nbgrader": { 176 | "grade": false, 177 | "grade_id": "cell-7c040f6c57dd2a26", 178 | "locked": true, 179 | "schema_version": 3, 180 | "solution": false, 181 | "task": false 182 | } 183 | }, 184 | "source": [ 185 | "## A1.ab: Execute basic bash commands in Python (using Jupyter) [20-30 min] TPS\n", 186 | "### ab.i Confirmation of basic bash operations
\n", 187 | "Usually, you would want to use command line in your terminal to run an R script for a given job/task. Here we are going to leverage the `%%bash` 'magic command' in the jupyter python kernel to execute bash commands in the notebok directly. More information on magic commands can be found in the [documentation of the python kernel](https://ipython.readthedocs.io/en/stable/interactive/magics.html). If you want to call bash commands using the R kernel, you will utilize the [`system`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/system) function in R.\n", 188 | "\n", 189 | "For example to execute the `pwd` command in the python kernel, you will use, \n", 190 | "\n", 191 | "```\n", 192 | "%%bash\n", 193 | "pwd\n", 194 | "```\n", 195 | "\n", 196 | "To execute the same `pwd` command in the R kernel, you will use, \n", 197 | "\n", 198 | "```\n", 199 | "system('pwd', intern=TRUE)\n", 200 | "```\n", 201 | "\n", 202 | "In this notebook, we will **only be using the python kernel**. We are doing this because the syntax for bash is easier and more concise under python than R. We will switch to the R kernel, which you have already installed in the configuration instructions, starting Week 3." 203 | ] 204 | }, 205 | { 206 | "cell_type": "markdown", 207 | "metadata": { 208 | "nbgrader": { 209 | "grade": false, 210 | "grade_id": "cell-c55032ae385a03ef", 211 | "locked": true, 212 | "schema_version": 3, 213 | "solution": false, 214 | "task": false 215 | } 216 | }, 217 | "source": [ 218 | "### ab.ii Continuation of basic bash operations
\n", 219 | "Use the basic command lines covered in lecture to walk through the following exercises" 220 | ] 221 | }, 222 | { 223 | "cell_type": "markdown", 224 | "metadata": { 225 | "nbgrader": { 226 | "grade": false, 227 | "grade_id": "cell-38caa9aecb01a4e0", 228 | "locked": true, 229 | "points": 1, 230 | "schema_version": 3, 231 | "solution": false, 232 | "task": true 233 | } 234 | }, 235 | "source": [ 236 | "#### Question 3 (1 point)\n", 237 | "Find and list the `artists.txt` file. \n", 238 | "=== BEGIN MARK SCHEME === \n", 239 | "```ruby\n", 240 | "%%bash\n", 241 | "ls data/art\n", 242 | "```\n", 243 | "```\n", 244 | "artists.txt\n", 245 | "```\n", 246 | "__Answer:__ artists.txt \n", 247 | "=== END MARK SCHEME === " 248 | ] 249 | }, 250 | { 251 | "cell_type": "code", 252 | "execution_count": 37, 253 | "metadata": { 254 | "nbgrader": { 255 | "grade": false, 256 | "grade_id": "cell-e335aad81b9fbd8f", 257 | "locked": false, 258 | "schema_version": 3, 259 | "solution": true, 260 | "task": false 261 | } 262 | }, 263 | "outputs": [ 264 | { 265 | "name": "stdout", 266 | "output_type": "stream", 267 | "text": [ 268 | "artists.txt\n" 269 | ] 270 | } 271 | ], 272 | "source": [ 273 | "%%bash\n", 274 | "### BEGIN MY SOLUTION\n", 275 | "ls data/art\n", 276 | "### END MY SOLUTION" 277 | ] 278 | }, 279 | { 280 | "cell_type": "markdown", 281 | "metadata": { 282 | "nbgrader": { 283 | "grade": false, 284 | "grade_id": "cell-7ec84fb290a57a6e", 285 | "locked": true, 286 | "points": 1, 287 | "schema_version": 3, 288 | "solution": false, 289 | "task": true 290 | } 291 | }, 292 | "source": [ 293 | "#### Question 4 (1 point)\n", 294 | "Count the number of artists in the file that are __not__ French. Print out this list. \n", 295 | "_Note: Insert cells below for your code and answer._ \n", 296 | "=== BEGIN MARK SCHEME === \n", 297 | "```ruby\n", 298 | "%%bash\n", 299 | "cd data/art \n", 300 | "grep -c -v French artists.txt\n", 301 | "```\n", 302 | "```\n", 303 | "138\n", 304 | "```\n", 305 | "__Answer:__ 138 \n", 306 | "=== END MARK SCHEME === \n", 307 | "\n", 308 | "Script your own task that includes 1-2 basic commands we haven't yet tried. \n", 309 | "_Note: Insert cells below for your code and answer._" 310 | ] 311 | }, 312 | { 313 | "cell_type": "markdown", 314 | "metadata": { 315 | "nbgrader": { 316 | "grade": false, 317 | "grade_id": "cell-b298e5fd54c5f6c4", 318 | "locked": true, 319 | "schema_version": 3, 320 | "solution": false, 321 | "task": false 322 | } 323 | }, 324 | "source": [ 325 | "### ab.iii Developing these skills on your own time \n", 326 | "\n", 327 | "Now that we've worked through these in pairs, try the following exercises on your own. Have them complete pior to next class.
" 328 | ] 329 | }, 330 | { 331 | "cell_type": "markdown", 332 | "metadata": { 333 | "nbgrader": { 334 | "grade": false, 335 | "grade_id": "cell-6b0a0d4ba495152a", 336 | "locked": true, 337 | "points": 1, 338 | "schema_version": 3, 339 | "solution": false, 340 | "task": true 341 | } 342 | }, 343 | "source": [ 344 | "##### Question 5 (1 point)\n", 345 | "Print the first 10 lines of `artists.txt` \n", 346 | "_Note: Insert cells below for your code and answer._ \n", 347 | "=== BEGIN MARK SCHEME === \n", 348 | "```ruby\n", 349 | "%%bash\n", 350 | "head data/art/artists.txt\n", 351 | "```\n", 352 | "```\n", 353 | "KILIAN, Wolfgang\t(1581-1662)\tBaroque\tGerman graphic artist (Augsburg)\n", 354 | "KINSOEN, François-Joseph\t(1771-1839)\tRomanticism\tFlemish painter\n", 355 | "KISS, August Karl Edouard\t(1802-1865)\tRomanticism\tGerman sculptor\n", 356 | "KISS, Bálint\t(1802-1868)\tRomanticism\tHungarian painter (Pest)\n", 357 | "KLEINER, Salomon\t(1703-1761)\tBaroque\tGerman graphic artist\n", 358 | "KLENZE, Leo von\t(1784-1864)\tRomanticism\tGerman architect\n", 359 | "KLESECKER, Justus (see GLESKER, Justus)\t(c. 1615-1678)\tBaroque\tGerman sculptor (Franconia)\n", 360 | "KLINGER, Max\t(1857-1920)\tRealism\tGerman painter\n", 361 | "KLOCKER, Hans\t(active 1478-1500l)\tNorthern Renaissance\tAustrian sculptor (South Tyrol)\n", 362 | "KLODT, Mikhail Konstantinovich\t(c. 1832-1902)\tRealism\tRussian painter (St. Petersburg)\n", 363 | "```\n", 364 | "=== END MARK SCHEME === \n", 365 | "\n", 366 | "Make a copy of `artists.txt` and rename it as `artists_new.txt`. Move the new copy to a new folder titled `new_folder` in the `data` folder (at the same level of the `art` folder.) \n", 367 | "_Note: Insert cells below for your code and answer._ \n", 368 | "=== BEGIN MARK SCHEME === \n", 369 | "```ruby\n", 370 | "%%bash\n", 371 | "cd data/\n", 372 | "mkdir new_folder\n", 373 | "cp art/artists.txt new_folder/artists_new.txt\n", 374 | "``` \n", 375 | "=== END MARK SCHEME === " 376 | ] 377 | }, 378 | { 379 | "cell_type": "markdown", 380 | "metadata": { 381 | "nbgrader": { 382 | "grade": false, 383 | "grade_id": "cell-ead93ee62631f746", 384 | "locked": true, 385 | "points": 1, 386 | "schema_version": 3, 387 | "solution": false, 388 | "task": true 389 | } 390 | }, 391 | "source": [ 392 | "#### Question 6 (1 point)\n", 393 | "Now, ask a question about the data, then answer it with your script! Create your own script returning some information about about the `artists.txt` file that we didn't know about before or haven't yet tried - Utilize the __`sort`__ command as part of your script. \n", 394 | "_Note: Insert cells below for your code and answer._ \n", 395 | "\n", 396 | "Reflections: On an integer scale of `1-5`, `1` being very easy and `5` being the most difficult, where would you rank today's exercises? Be honest! It's okay if you put a `5`, and will help us better understand how to make sure your needs are being met. " 397 | ] 398 | }, 399 | { 400 | "cell_type": "markdown", 401 | "metadata": { 402 | "nbgrader": { 403 | "grade": false, 404 | "grade_id": "cell-c48add631e5a7194", 405 | "locked": true, 406 | "schema_version": 3, 407 | "solution": false, 408 | "task": false 409 | } 410 | }, 411 | "source": [ 412 | "## A1.ba: Wildcards, redirections, and pipes [20-30 min] Group of 3 \n", 413 | "### ba.i Glob\n", 414 | "What is glob, and why use it compared to basic command line functions?" 415 | ] 416 | }, 417 | { 418 | "cell_type": "markdown", 419 | "metadata": { 420 | "nbgrader": { 421 | "grade": false, 422 | "grade_id": "cell-8e3c252192e9c58f", 423 | "locked": true, 424 | "points": 1, 425 | "schema_version": 3, 426 | "solution": false, 427 | "task": true 428 | } 429 | }, 430 | "source": [ 431 | "#### Question 7 (1 point)\n", 432 | "Utliize glob to create a command that lists all the .txt files in the `tmp` directory, located in `data`. What could be another way to glob? Include this answer as a few sentences. \n", 433 | "_Note: Insert cells below for your code and answer._ \n", 434 | "=== BEGIN MARK SCHEME === \n", 435 | "```ruby\n", 436 | "%%bash\n", 437 | "ls data/tmp/*.txt\n", 438 | "```\n", 439 | "=== END MARK SCHEME === " 440 | ] 441 | }, 442 | { 443 | "cell_type": "markdown", 444 | "metadata": { 445 | "nbgrader": { 446 | "grade": false, 447 | "grade_id": "cell-d78e7ace05ce7481", 448 | "locked": true, 449 | "schema_version": 3, 450 | "solution": false, 451 | "task": false 452 | } 453 | }, 454 | "source": [ 455 | "### ba.i Redirection and pipes \n", 456 | "In your, work on these individually and then compare your scripts.\n", 457 | "What does it mean to redirect, and why would you utilize a pipe over a basic command line?" 458 | ] 459 | }, 460 | { 461 | "cell_type": "markdown", 462 | "metadata": { 463 | "nbgrader": { 464 | "grade": false, 465 | "grade_id": "cell-2896a8740be4aeb4", 466 | "locked": true, 467 | "points": 1, 468 | "schema_version": 3, 469 | "solution": false, 470 | "task": true 471 | } 472 | }, 473 | "source": [ 474 | "#### Question 8 (1 point)\n", 475 | "Building off of glob, use a pipe to count the number of .txt files in `data/tmp` \n", 476 | "_Note: Insert cells below for your code and answer._ \n", 477 | "=== BEGIN MARK SCHEME === \n", 478 | "```ruby\n", 479 | "%%bash\n", 480 | "ls data/tmp/*.txt | wc -l\n", 481 | "```\n", 482 | "```\n", 483 | "191\n", 484 | "```\n", 485 | "=== END MARK SCHEME === \n", 486 | "\n", 487 | "Now, redirect the counted number as a saved `file_number.txt` file to the `new_folder` directory. What happens to the file if you repeat the same task, but exclude the pipe (name this `file_list.txt` so you can compare)? \n", 488 | "_Note: Insert cells below for your code and answer._ \n", 489 | "=== BEGIN MARK SCHEME === \n", 490 | "```ruby\n", 491 | "%%bash\n", 492 | "ls data/tmp/*.txt | wc -l > data/new_folder/file_number.txt\n", 493 | "ls data/tmp/*.txt > data/new_folder/file_list.txt\n", 494 | "```\n", 495 | "=== END MARK SCHEME === \n", 496 | "\n", 497 | "How do your scripts compare or differ, either in input (command) or output? \n", 498 | "_Note: Insert cells below for your code and answer._" 499 | ] 500 | }, 501 | { 502 | "cell_type": "markdown", 503 | "metadata": { 504 | "nbgrader": { 505 | "grade": false, 506 | "grade_id": "cell-6c262fbd792007e8", 507 | "locked": true, 508 | "schema_version": 3, 509 | "solution": false, 510 | "task": false 511 | } 512 | }, 513 | "source": [ 514 | "### A1.bb: Affirming what you learned in Week 1 [20-30 min, assignment] Individual" 515 | ] 516 | }, 517 | { 518 | "cell_type": "markdown", 519 | "metadata": { 520 | "nbgrader": { 521 | "grade": false, 522 | "grade_id": "cell-0707e5dd07851e1b", 523 | "locked": true, 524 | "points": 1, 525 | "schema_version": 3, 526 | "solution": false, 527 | "task": true 528 | } 529 | }, 530 | "source": [ 531 | "#### Question 9 (1 point)\n", 532 | "What is the distinction between an absolute vs relative file path? Script an example of these two comparison along with a brief written answer. \n", 533 | "_Note: Insert cells below for your code and answer._ \n", 534 | "=== BEGIN MARK SCHEME === \n", 535 | "```ruby\n", 536 | "%%bash\n", 537 | "cd data/tmp/\n", 538 | "pwd\n", 539 | "cd .\n", 540 | "pwd\n", 541 | "``` \n", 542 | "```\n", 543 | "/Users/sulhasan/Downloads/HW-Keys/data/tmp\n", 544 | "/Users/sulhasan/Downloads/HW-Keys/data/tmp\n", 545 | "```\n", 546 | "=== END MARK SCHEME === \n", 547 | "\n", 548 | "What are 3 ways you can extend the __`ls`__ command to give you more information, and what do they give? \n", 549 | "_Note: Insert cells below for your code and answer._ \n", 550 | "=== BEGIN MARK SCHEME === \n", 551 | "```ruby\n", 552 | "%%bash\n", 553 | "ls data/tmp/\n", 554 | "ls -F data/tmp/\n", 555 | "ls -a data/tmp/\n", 556 | "man ls\n", 557 | "``` \n", 558 | "=== END MARK SCHEME === " 559 | ] 560 | }, 561 | { 562 | "cell_type": "markdown", 563 | "metadata": { 564 | "nbgrader": { 565 | "grade": false, 566 | "grade_id": "cell-0707e5dd07851e1c", 567 | "locked": true, 568 | "points": 1, 569 | "schema_version": 3, 570 | "solution": false, 571 | "task": true 572 | } 573 | }, 574 | "source": [ 575 | "#### Question 10 (1 point)\n", 576 | "Create a file named `test.txt`, move it into the `new_folder`, then delete the file. \n", 577 | "_Note: Insert cells below for your code and answer._ \n", 578 | "=== BEGIN MARK SCHEME === \n", 579 | "```ruby\n", 580 | "%%bash\n", 581 | "touch data/new_folder/test.txt\n", 582 | "rm data/new_folder/test.txt\n", 583 | "``` \n", 584 | "=== END MARK SCHEME === \n", 585 | "\n", 586 | "Create a sorted file artists (alphabetical order) from `artists.txt` labeled as `artists_sorted.txt` and place it in the `new_folder`. Then identify the number of unique artists in that file. \n", 587 | "_Note: Insert cells below for your code and answer._ \n", 588 | "=== BEGIN MARK SCHEME === \n", 589 | "```ruby\n", 590 | "%%bash\n", 591 | "sort data/art/artists.txt > data/new_folder/artists_sorted.txt\n", 592 | "uniq -c data/new_folder/artists_sorted.txt\n", 593 | "``` \n", 594 | "=== END MARK SCHEME === " 595 | ] 596 | }, 597 | { 598 | "cell_type": "markdown", 599 | "metadata": { 600 | "nbgrader": { 601 | "grade": false, 602 | "grade_id": "cell-6a0f3f735605085", 603 | "locked": true, 604 | "points": 1, 605 | "schema_version": 3, 606 | "solution": false, 607 | "task": true 608 | } 609 | }, 610 | "source": [ 611 | "#### Question 11 (1 point)\n", 612 | "Use __`nano`__ in your terminal (not jupyter notebook) to create a bash script titled `print_names.sh` that echos any name entered in a list of 4 names (3 of the names are fixed, the 4th is not). Move the script to `new_folder`, then run it. Take a screenshot of the input to run the script and output. Briefly explain why you have to do this on terminal, and can't run this on your Jupyter notebook? \n", 613 | "_Note: Insert cells below for your code and answer._ \n", 614 | "=== BEGIN MARK SCHEME === \n", 615 | "```ruby\n", 616 | "%%bash\n", 617 | "cat print_names.sh\n", 618 | "```\n", 619 | "```\n", 620 | "# !/usr/bin/env bash\n", 621 | "# Filename: print_names.sh\n", 622 | "\n", 623 | "echo \"Please type in your name:\"\n", 624 | "read new_name\n", 625 | "\n", 626 | "echo \"Alice\"\n", 627 | "echo \"Bob\"\n", 628 | "echo \"Cathy\"\n", 629 | "echo $new_name\n", 630 | "```\n", 631 | "=== END MARK SCHEME ===" 632 | ] 633 | }, 634 | { 635 | "cell_type": "markdown", 636 | "metadata": { 637 | "nbgrader": { 638 | "grade": false, 639 | "grade_id": "cell-48971fe0ad961c93", 640 | "locked": true, 641 | "points": 1, 642 | "schema_version": 3, 643 | "solution": false, 644 | "task": true 645 | } 646 | }, 647 | "source": [ 648 | "#### Question 12 (1 point)\n", 649 | "Use __`nano`__ to create your own script that uses 2 commands we've used and 1 command we haven't yet used (3 total, but you can include more if you'd like) that answers another question you have about the contents of the `artists.txt` file. Label this script as `artist_text.sh` and place it in `new_folder`. Describe what it does, and how. \n", 650 | "_Note: Insert cells below for your code and answer._\n", 651 | "\n", 652 | "Reflections: On an integer scale of `1-5`, `1` being very easy and `5` being the most difficult, where would you rank the A1.bb assignment and why? Include some notes about what you gained from this past week that you didn't know before as well as notes of things you already knew.\n", 653 | "\n", 654 | "Improvements: Notice a [potentially intentional] mistake, or an area of this homework that could have been improved? Include your thoughts here. " 655 | ] 656 | } 657 | ], 658 | "metadata": { 659 | "celltoolbar": "Create Assignment", 660 | "kernelspec": { 661 | "display_name": "Python 3", 662 | "language": "python", 663 | "name": "python3" 664 | }, 665 | "language_info": { 666 | "codemirror_mode": { 667 | "name": "ipython", 668 | "version": 3 669 | }, 670 | "file_extension": ".py", 671 | "mimetype": "text/x-python", 672 | "name": "python", 673 | "nbconvert_exporter": "python", 674 | "pygments_lexer": "ipython3", 675 | "version": "3.6.3" 676 | } 677 | }, 678 | "nbformat": 4, 679 | "nbformat_minor": 4 680 | } 681 | -------------------------------------------------------------------------------- /Homework/HW2-Key_Scripting+Jobs_Bash.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": { 6 | "nbgrader": { 7 | "grade": false, 8 | "grade_id": "cell-8531b0dab318b0d2", 9 | "locked": true, 10 | "schema_version": 3, 11 | "solution": false, 12 | "task": false 13 | } 14 | }, 15 | "source": [ 16 | "# Homework 2: Scripting and Jobs (Bash, cnt'd)\n", 17 | "Curated by Sabah Ul-Hasan, Huitian Dao, Shang-Fu Chen, Karthik Gangavarapu, and Andrew Su\n", 18 | "\n", 19 | "Complete homework is due every Tuesday at 8 AM PST.
\n", 20 | "Save your homework as you go, so the efforts don't get lost.
\n", 21 | "Note there are up 12 points, but you can only receive 10 points total for homework.\n", 22 | "\n", 23 | "In this assignment, you will
\n", 24 | "A2.aa Refresh your understanding of bash
\n", 25 | "A2.ab Explore pipes in-depth (+awk)
\n", 26 | "A2.ba Familiarize yourself with loops
\n", 27 | "A2.bb Compile what you've learned as a script
\n", 28 | "\n", 29 | "Note that there is a section at the end (A2.bb) to point out any enhancements you personally would make to this assignment if you were to lead the course. " 30 | ] 31 | }, 32 | { 33 | "cell_type": "markdown", 34 | "metadata": { 35 | "nbgrader": { 36 | "grade": false, 37 | "grade_id": "cell-e3c9da73e2811a39", 38 | "locked": true, 39 | "schema_version": 3, 40 | "solution": false, 41 | "task": false 42 | } 43 | }, 44 | "source": [ 45 | "## A2.aa: Refresh understanding of bash [20-30 min] Group of 4 " 46 | ] 47 | }, 48 | { 49 | "cell_type": "markdown", 50 | "metadata": { 51 | "nbgrader": { 52 | "grade": false, 53 | "grade_id": "cell-c2f549622733ffcc", 54 | "locked": true, 55 | "points": 1, 56 | "schema_version": 3, 57 | "solution": false, 58 | "task": true 59 | } 60 | }, 61 | "source": [ 62 | "#### Question 1 (1 point) [5 min]\n", 63 | "In your group, identify four items you each considered to be the most difficult part of Homework 1. Then, break into pairs based on who in the group found it easier to navigate vs harder to navigate. In other words, pair yourself with someone who better understood what you found difficult and vice versa. Denote what these sections are below as a,b,c,or d." 64 | ] 65 | }, 66 | { 67 | "cell_type": "markdown", 68 | "metadata": { 69 | "nbgrader": { 70 | "grade": false, 71 | "grade_id": "cell-33e455f553bdbc47", 72 | "locked": true, 73 | "points": 1, 74 | "schema_version": 3, 75 | "solution": false, 76 | "task": true 77 | } 78 | }, 79 | "source": [ 80 | "#### Question 2 (1 point) [10 min, 15 min]\n", 81 | "Spend time discussing your troubleshooting process of working through what the other person found as difficult with one another. Write down what you learned. What was the before vs after result?\n", 82 | "Then, share as a whole group. Write down what you gained from the discussion in how you will be approaching bash scripting differently than you would do before." 83 | ] 84 | }, 85 | { 86 | "cell_type": "markdown", 87 | "metadata": { 88 | "nbgrader": { 89 | "grade": false, 90 | "grade_id": "cell-0948135824f7008f", 91 | "locked": true, 92 | "schema_version": 3, 93 | "solution": false, 94 | "task": false 95 | } 96 | }, 97 | "source": [ 98 | "## A2.aa: Explore pipes in-depth (+awk) [20-30 min] TPS \n", 99 | "- On your own time, try the following exercises [10-15 min]" 100 | ] 101 | }, 102 | { 103 | "cell_type": "markdown", 104 | "metadata": { 105 | "nbgrader": { 106 | "grade": false, 107 | "grade_id": "cell-1ff35e1dfe3e898b", 108 | "locked": true, 109 | "points": 1, 110 | "schema_version": 3, 111 | "solution": false, 112 | "task": true 113 | } 114 | }, 115 | "source": [ 116 | "#### Question 3 (1 point)\n", 117 | "Describe your current understanding of pipes. What are the various approaches, where does __`awk`__ come into play?\n", 118 | "\n", 119 | "=== BEGIN MARK SCHEME === \n", 120 | "- Pipe is used to connect STDOUT to STDIN \n", 121 | "- __`awk`__ can be used to process text files, especially delimited files based on seperated fields. \n", 122 | "\n", 123 | "=== END MARK SCHEME ===\n", 124 | "\n", 125 | "Find the error and fix to run the script. Describe the error in a sentence. What is `{print $3}` doing? Describe what awk is doing this, and its limitations in recognizing delimiters (Hint: tab). \n", 126 | "\n", 127 | "```ruby\n", 128 | "%%bash\n", 129 | "awk '{print $3}' data/new_folder/artists_new.txt\n", 130 | "```\n", 131 | "\n", 132 | "=== BEGIN MARK SCHEME === \n", 133 | "```ruby\n", 134 | "%%bash\n", 135 | "# Need to set the field seperator as tab\n", 136 | "awk -F \"\\t\" '{print $3}' data/new_folder/artists_new.txt\n", 137 | "```\n", 138 | "=== END MARK SCHEME ===" 139 | ] 140 | }, 141 | { 142 | "cell_type": "markdown", 143 | "metadata": { 144 | "nbgrader": { 145 | "grade": false, 146 | "grade_id": "cell-a1d79798122352a1", 147 | "locked": true, 148 | "points": 1, 149 | "schema_version": 3, 150 | "solution": false, 151 | "task": true 152 | } 153 | }, 154 | "source": [ 155 | "#### Question 4 (1 point) [10-15 min]\n", 156 | "Use __`awk`__, __`sort`__, and/or __`uniq`__ to find the most common last names among all artists in `artists.txt` \n", 157 | "Now, discuss your findings with your partner. What was similar, and what was different?\n", 158 | "\n", 159 | "=== BEGIN MARK SCHEME === \n", 160 | "```ruby\n", 161 | "%%bash\n", 162 | "# 3\n", 163 | "awk -F \",| \" '{print $1}' data/new_folder/artists_new.txt | uniq -c | sort -r | head\n", 164 | "```\n", 165 | "```\n", 166 | " 5 KOBELL\n", 167 | " 5 KNIP\n", 168 | " 4 KONINCK\n", 169 | " 4 ALBERTI\n", 170 | " 4 ADAM\n", 171 | " 3 TENIERS\n", 172 | " 3 TARAVAL\n", 173 | " 3 AGOSTINO\n", 174 | " 3 AGNOLO\n", 175 | " 2 TESSIN\n", 176 | "```\n", 177 | "=== END MARK SCHEME ===" 178 | ] 179 | }, 180 | { 181 | "cell_type": "markdown", 182 | "metadata": { 183 | "nbgrader": { 184 | "grade": false, 185 | "grade_id": "cell-4e1133a9dd69b7b5", 186 | "locked": true, 187 | "schema_version": 3, 188 | "solution": false, 189 | "task": false 190 | } 191 | }, 192 | "source": [ 193 | "On your own: " 194 | ] 195 | }, 196 | { 197 | "cell_type": "markdown", 198 | "metadata": { 199 | "nbgrader": { 200 | "grade": false, 201 | "grade_id": "cell-300b78e3db68717f", 202 | "locked": true, 203 | "points": 1, 204 | "schema_version": 3, 205 | "solution": false, 206 | "task": true 207 | } 208 | }, 209 | "source": [ 210 | "#### Question 5 (1 point)\n", 211 | "Now that we've worked through these in pairs, create a bash script that integrates two items we haven't yet tried in the exercises, such as __`NF`__, to answer a question about the `artists.txt` file. Describe briefly what this does. Have this complete pior to next class.\n", 212 | "\n", 213 | "=== BEGIN MARK SCHEME === \n", 214 | "__Example:__ Using different field seperators, find out how many rows have certain number of columns\n", 215 | "\n", 216 | "\n", 217 | "```ruby\n", 218 | "%%bash\n", 219 | "awk -F '\\t' '{print NF}' data/new_folder/artists_new.txt | sort | uniq -c\n", 220 | "```\n", 221 | "```\n", 222 | "150 4\n", 223 | "```\n", 224 | "\n", 225 | "```ruby\n", 226 | "%%bash\n", 227 | "awk -F ',' '{print NF}' data/new_folder/artists_new.txt | sort | uniq -c\n", 228 | "```\n", 229 | "```\n", 230 | " 10 1\n", 231 | " 128 2\n", 232 | " 12 3\n", 233 | "```\n", 234 | "=== END MARK SCHEME ===\n", 235 | "\n", 236 | "Reflections: On an integer scale of 1-5, 1 being very easy and 5 being the most difficult, where would you rank today's exercises? Provide brief notes on what was easy vs difficult, and why. \n", 237 | "\n", 238 | "=== BEGIN MARK SCHEME === \n", 239 | "\n", 240 | "=== END MARK SCHEME ===" 241 | ] 242 | }, 243 | { 244 | "cell_type": "markdown", 245 | "metadata": { 246 | "nbgrader": { 247 | "grade": false, 248 | "grade_id": "cell-e30a29557264afab", 249 | "locked": true, 250 | "schema_version": 3, 251 | "solution": false, 252 | "task": false 253 | } 254 | }, 255 | "source": [ 256 | "## A2.ba: Loops [20-30 min] Group of 3\n", 257 | "### ba.i Loops [10 min]\n", 258 | "On your own" 259 | ] 260 | }, 261 | { 262 | "cell_type": "markdown", 263 | "metadata": { 264 | "nbgrader": { 265 | "grade": false, 266 | "grade_id": "cell-6a789383b1f6dddd", 267 | "locked": true, 268 | "points": 1, 269 | "schema_version": 3, 270 | "solution": false, 271 | "task": true 272 | } 273 | }, 274 | "source": [ 275 | "#### Question 6 (1 point)\n", 276 | "Describe how a loop operates. Why and when do you want to use a loop, vs a single command string?\n", 277 | "\n", 278 | "=== BEGIN MARK SCHEME === \n", 279 | "\n", 280 | "__Loop:__\n", 281 | "1. A sequence of instructions to be repeated until a certain condition is reached\n", 282 | "1. Why: to conveniently repeat instructions\n", 283 | "1. When: when an instruction need to be executed repeatedly and the condition for ending executioncan be described \n", 284 | "\n", 285 | "=== END MARK SCHEME ===\n", 286 | "\n", 287 | "Write a bash for loop that outpouts letters a-e\n", 288 | "\n", 289 | "=== BEGIN MARK SCHEME === \n", 290 | "```ruby\n", 291 | "%%bash\n", 292 | "# 2\n", 293 | "for i in {a..e}\n", 294 | "do\n", 295 | " echo $i\n", 296 | "done\n", 297 | "```\n", 298 | "```\n", 299 | "a\n", 300 | "b\n", 301 | "c\n", 302 | "d\n", 303 | "e\n", 304 | "```\n", 305 | "=== END MARK SCHEME ===" 306 | ] 307 | }, 308 | { 309 | "cell_type": "markdown", 310 | "metadata": { 311 | "nbgrader": { 312 | "grade": false, 313 | "grade_id": "cell-8707f4ad4abb75b7", 314 | "locked": true, 315 | "points": 1, 316 | "schema_version": 3, 317 | "solution": false, 318 | "task": true 319 | } 320 | }, 321 | "source": [ 322 | "#### Question 7 (1 point)\n", 323 | "What are the different types of loops, and when might you want to try one over another? Script an example.\n", 324 | "\n", 325 | "=== BEGIN MARK SCHEME === \n", 326 | "1. __For loop__\n", 327 | "\n", 328 | "```ruby\n", 329 | "%%bash\n", 330 | "# For / While / Util\n", 331 | "\n", 332 | "for i in {1..3}\n", 333 | "do\n", 334 | " echo ${i}\n", 335 | "done\n", 336 | "```\n", 337 | "```\n", 338 | "1\n", 339 | "2\n", 340 | "3\n", 341 | "```\n", 342 | "\n", 343 | "2. __While loop__\n", 344 | "\n", 345 | "```ruby\n", 346 | "%%bash\n", 347 | "i=0\n", 348 | "\n", 349 | "while [ ${i} -lt 3 ]\n", 350 | "do\n", 351 | " echo ${i}\n", 352 | " i=$((i+1))\n", 353 | "done\n", 354 | "```\n", 355 | "```\n", 356 | "0\n", 357 | "1\n", 358 | "2\n", 359 | "```\n", 360 | "\n", 361 | "3. __Until loop__ \n", 362 | "\n", 363 | "```ruby\n", 364 | "%%bash\n", 365 | "i=0\n", 366 | "\n", 367 | "until [ ${i} -gt 3 ]\n", 368 | "do\n", 369 | " echo ${i}\n", 370 | " i=$((i+1))\n", 371 | "done\n", 372 | "```\n", 373 | "```\n", 374 | "0\n", 375 | "1\n", 376 | "2\n", 377 | "3\n", 378 | "```\n", 379 | "\n", 380 | "=== END MARK SCHEME ===" 381 | ] 382 | }, 383 | { 384 | "cell_type": "markdown", 385 | "metadata": { 386 | "nbgrader": { 387 | "grade": false, 388 | "grade_id": "cell-fe05faaf91b75713", 389 | "locked": true, 390 | "schema_version": 3, 391 | "solution": false, 392 | "task": false 393 | } 394 | }, 395 | "source": [ 396 | "### A2.bb: Create a script to run a job [20-30 min] Individual\n", 397 | "Get excited, we're about to apply what we've learned from a technical perspective to the science-y stuff! Familiar with 'fasta files' from NCBI? Here we go!\n", 398 | "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp\n", 399 | "\n", 400 | "#### bb.i Applying what we've learned on bash to biology
" 401 | ] 402 | }, 403 | { 404 | "cell_type": "markdown", 405 | "metadata": { 406 | "nbgrader": { 407 | "grade": false, 408 | "grade_id": "cell-ddee5afbc0429aee", 409 | "locked": true, 410 | "points": 1, 411 | "schema_version": 3, 412 | "solution": false, 413 | "task": true 414 | } 415 | }, 416 | "source": [ 417 | "#### Question 8 (1 point)\n", 418 | "In your \"Applied-Bioinformatics_Course\" Github repository, create a folder titled \"HW2_[Lastname]\" \n", 419 | "_Note: Always check that you're in the correct working directory_\n", 420 | "\n", 421 | "Create a bash loop that renames all the files in the folder data/fastq folder from `*.fq` to `*.fastq` \n", 422 | "_Note: Have all these files copied and moved into the `new_folder` directory so as not to overwrite the original `*.fq`_\n", 423 | "\n", 424 | "=== BEGIN MARK SCHEME === \n", 425 | "```ruby\n", 426 | "%%bash\n", 427 | "# 2\n", 428 | "\n", 429 | "cp -R data/fastq data/new_folder\n", 430 | "pwd\n", 431 | "cd data/new_folder/fastq\n", 432 | "\n", 433 | "for i in *.fq\n", 434 | "do\n", 435 | " mv $i ${i/.fq/.fastq} \n", 436 | "done\n", 437 | "```\n", 438 | "```\n", 439 | "/Users/sulhasan/Downloads/HW-Keys\n", 440 | "```\n", 441 | "=== END MARK SCHEME ===" 442 | ] 443 | }, 444 | { 445 | "cell_type": "markdown", 446 | "metadata": { 447 | "nbgrader": { 448 | "grade": false, 449 | "grade_id": "cell-24812d415f3fdeac", 450 | "locked": true, 451 | "points": 1, 452 | "schema_version": 3, 453 | "solution": false, 454 | "task": true 455 | } 456 | }, 457 | "source": [ 458 | "#### Question 9 (1 point)\n", 459 | "Print all nucleotide sequences from ./data/fastq/simulated1.R1.fastq by replacing all 'T's in the nucleotide sequences with 'U's\n", 460 | "\n", 461 | "=== BEGIN MARK SCHEME === \n", 462 | "```ruby\n", 463 | "%%bash\n", 464 | "cat data/new_folder/fastq/simulated1.R1.fastq | awk \"NR%4==2\" | tr T U\n", 465 | "```\n", 466 | "```\n", 467 | "UGGGAAAACCAGGAGAGUUCUUCCUGAAAUAGUCCGUGAAGCCAUAAAAAGAAGACUCCGUACUGUGAUC\n", 468 | "ACUUACCAUUUGUCAUGGCCCUGGGACUAACCGCUGUGAGGCUGGUCGACCCGAUCAACGUGGUGGGACU\n", 469 | "GCCAGACAACCCCGUUUAUUAGAGAGGACGCUGACCCUUGUGUGGGGGCCUCAUAGCUUCCAUGGUAAGC\n", 470 | "CUCUAAGCUGAUGCUGGAACUUGAUCCACCAUUUGGGGACUCUUACAUUGUCAUAGGAGUCGGGGAGAAG\n", 471 | "GGCAUCACCGAGGUGUGCAGAGAAGAGGCCCGCCGCGCCCUCAAGGACGGUGUGGCAACGGGAGGCCAUG\n", 472 | "GAGAUUGCCCGUGCCUGUGAACGAGCUGCCCCACGGGUGGAAGGCUUUGGGGAAAUCGUAUUUCGUCAGA\n", 473 | "AUACCAUCAUCCCAGGCUUGCUUGACUGCUGCUGGCAAUCUACGGGGGGAGUCAGGAUGGUACUUGUACC\n", 474 | "UUCUUCUUCACACUGCCUUUUCCCUUCAGAGAGAGGAGCAAAAACCCCCCGCAAGUAGCAAGGCCUGCUC\n", 475 | "GAAAGAUCUGGCUGCCAAGCUGAGAAUAAUCAAUGCUAGGAAGGAGAAGAAGAGACGAGGCGCAGAUACU\n", 476 | "GUUUUCAAGGAAAAAGUGGACACUAGGGUGCCAGACCCCCAAGAAGGCACUCGUCAGGUUAUGAGCAUGG\n", 477 | "ACAUGCAAACUCUGACCCCAGUUGGGAGGUUGAUAACCGCUAACCCCGUACUCACUGAAAGCACUGAGAA\n", 478 | "GGCUUGAAAAAAGACCAGGAGCCUUUUGUAUAAAAGUGUUGUGCCCAUACACCAGCACUAUGCUGGAAAC\n", 479 | "UCUUUUCUCUUUUUCCCAUCAUGUUGUACACACAGCUCUGGCACUCUCCUCUCAGGUGGUGCACUCUUUG\n", 480 | "CACUGAUUUGAAAGGUGCUCCAAAAAUUUGAUGGAUGCGCUUGCCCAAUGAGUUGAGAGCGCCUCCAACU\n", 481 | "CUUUUCCGCUCCCCCUUUGGUCUUGUCUCGAAAUAAUGUCCAUAACUGUUUUCCCUUUUUCAGCUGGUCU\n", 482 | "UAGAGUUCUCAGUUCUUUCAGUGAUUACGGGGUUAGCUGUUAUCAACCUCCCAACUGGGGUCAGAGUUUG\n", 483 | "ACUCUUAAUACGGACUAUGAUCCACCCAUAGCUUUGCACCAACACGGGUUCUUCAUGACCAGGGCCUCCU\n", 484 | "CCAGCCAGAAUUGCAUGUGUCCACAUUGUUGUGUUCCUAUUGCUGGUGGUGCUCAUACCUGAGCCAGAAA\n", 485 | "GAAUGACUCUCUCGCCAUCAAGAAUGACCGGCUUUAGGCAUCUCCUGGAAUCUAUGACACGGUCAGCUUU\n", 486 | "UUGAACGAGGAUCACUGGAUGUGGAGAUAGAACACAGGAGGUGGUGUUUAAGGGCUGGGAUUACAAAGAC\n", 487 | "```\n", 488 | "=== END MARK SCHEME ===" 489 | ] 490 | }, 491 | { 492 | "cell_type": "markdown", 493 | "metadata": { 494 | "nbgrader": { 495 | "grade": false, 496 | "grade_id": "cell-d806d7b7c1a25af3", 497 | "locked": true, 498 | "points": 1, 499 | "schema_version": 3, 500 | "solution": false, 501 | "task": true 502 | } 503 | }, 504 | "source": [ 505 | "#### Question 10 (1 point)\n", 506 | "Create a bash loop that renames all the files in the folder data/fastq folder from `*.fq` to `*.fastq` \n", 507 | "_Note: Have all these files copied and moved into the `new_folder` directory so as not to overwrite the original `*.fq`_\n", 508 | "\n", 509 | "=== BEGIN MARK SCHEME === \n", 510 | "```ruby\n", 511 | "%%bash\n", 512 | "\n", 513 | "cp -R data/fastq data/new_folder\n", 514 | "pwd\n", 515 | "cd data/new_folder/fastq\n", 516 | "\n", 517 | "for i in *.fq\n", 518 | "do\n", 519 | " mv $i ${i/.fq/.fastq} \n", 520 | "done\n", 521 | "```\n", 522 | "```\n", 523 | "/Users/sulhasan/Downloads/HW-Keys\n", 524 | "```\n", 525 | "=== END MARK SCHEME ===" 526 | ] 527 | }, 528 | { 529 | "cell_type": "markdown", 530 | "metadata": { 531 | "nbgrader": { 532 | "grade": false, 533 | "grade_id": "cell-383a0643090d29f1", 534 | "locked": true, 535 | "schema_version": 3, 536 | "solution": false, 537 | "task": false 538 | } 539 | }, 540 | "source": [ 541 | "#### Question 11 (1 point)
\n", 542 | "Reflections: On an integer scale of 1-5, 1 being very easy and 5 being the most difficult, where would you rank the A2.bb assignment and why? Include some notes about what you gained from this past week that you didn't know before as well as notes of things you already knew. \n", 543 | "\n", 544 | "Improvements: Notice a [potentially intentional] mistake, or an area of this homework that could have been improved? Include your thoughts here. " 545 | ] 546 | } 547 | ], 548 | "metadata": { 549 | "celltoolbar": "Create Assignment", 550 | "kernelspec": { 551 | "display_name": "Python 3", 552 | "language": "python", 553 | "name": "python3" 554 | }, 555 | "language_info": { 556 | "codemirror_mode": { 557 | "name": "ipython", 558 | "version": 3 559 | }, 560 | "file_extension": ".py", 561 | "mimetype": "text/x-python", 562 | "name": "python", 563 | "nbconvert_exporter": "python", 564 | "pygments_lexer": "ipython3", 565 | "version": "3.6.3" 566 | } 567 | }, 568 | "nbformat": 4, 569 | "nbformat_minor": 4 570 | } 571 | -------------------------------------------------------------------------------- /Homework/HW5-Key_Advanced-Plotting+RNA-Seq_R.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": {}, 6 | "source": [ 7 | "Before you turn this problem in, make sure everything runs as expected. First, **restart the kernel** (in the menubar, select Kernel$\\rightarrow$Restart) and then **run all cells** (in the menubar, select Cell$\\rightarrow$Run All).\n", 8 | "\n", 9 | "Make sure you fill in any place that says `YOUR CODE HERE` or \"YOUR ANSWER HERE\", as well as your name and collaborators below:" 10 | ] 11 | }, 12 | { 13 | "cell_type": "code", 14 | "execution_count": null, 15 | "metadata": {}, 16 | "outputs": [], 17 | "source": [ 18 | "NAME = \"\"\n", 19 | "COLLABORATORS = \"\"" 20 | ] 21 | }, 22 | { 23 | "cell_type": "markdown", 24 | "metadata": {}, 25 | "source": [ 26 | "---" 27 | ] 28 | }, 29 | { 30 | "cell_type": "markdown", 31 | "metadata": { 32 | "deletable": false, 33 | "editable": false, 34 | "nbgrader": { 35 | "cell_type": "markdown", 36 | "checksum": "af19bec3afb964774d85c2c4da8ad95c", 37 | "grade": false, 38 | "grade_id": "cell-b0209166ce6b4d54", 39 | "locked": true, 40 | "schema_version": 3, 41 | "solution": false, 42 | "task": false 43 | } 44 | }, 45 | "source": [ 46 | "# Homework 5: Advanced Plotting and RNA-Seq in R\n", 47 | "Curated by Sabah Ul-Hasan, Huitian Diao, Shang-Fu Chen, Jerry Zak, and Andrew Su\n", 48 | "\n", 49 | "Complete homework is due every Tuesday at 8 AM PST.
\n", 50 | "Save your homework as you go, so the efforts don't get lost.
\n", 51 | "Note there are up 11 points, but you can only receive 10 points total for homework.\n", 52 | "\n", 53 | "In this assignment, you will
\n", 54 | "A5.aa Affirm your understanding of R
\n", 55 | "A5.ab Expand and detail familarity with plotitng publishable figures in R
\n", 56 | "A5.ba Famliarize yourself with the end-goal figures general RNA-Seq analysis
\n", 57 | "A5.bb Practice application and build upon it in R\n", 58 | "\n", 59 | "Note that there is a section at the end (A5.bb) to point out any enhancements you personally would make to this assignment if you were to lead the course\n", 60 | "\n", 61 | "NOTE: Execute the code cell below to import the `testthat` library before you started working on the questions." 62 | ] 63 | }, 64 | { 65 | "cell_type": "code", 66 | "execution_count": null, 67 | "metadata": { 68 | "deletable": false, 69 | "editable": false, 70 | "nbgrader": { 71 | "cell_type": "code", 72 | "checksum": "200161fda2c997296658210cc89b72fa", 73 | "grade": false, 74 | "grade_id": "cell-711e732d8e1e849d", 75 | "locked": true, 76 | "schema_version": 3, 77 | "solution": false, 78 | "task": false 79 | } 80 | }, 81 | "outputs": [], 82 | "source": [ 83 | "# Import the required R library for test case and autograding\n", 84 | "library(testthat)" 85 | ] 86 | }, 87 | { 88 | "cell_type": "markdown", 89 | "metadata": { 90 | "deletable": false, 91 | "editable": false, 92 | "nbgrader": { 93 | "cell_type": "markdown", 94 | "checksum": "4905672cc1105ca2d7279d2d96eda8f7", 95 | "grade": false, 96 | "grade_id": "cell-9cbd0b1b17477028", 97 | "locked": true, 98 | "schema_version": 3, 99 | "solution": false, 100 | "task": false 101 | } 102 | }, 103 | "source": [ 104 | "## A5.aa: Affirm your understanding of R [20-30 min] Group of 3 " 105 | ] 106 | }, 107 | { 108 | "cell_type": "markdown", 109 | "metadata": { 110 | "deletable": false, 111 | "editable": false, 112 | "nbgrader": { 113 | "cell_type": "markdown", 114 | "checksum": "a92d63918b9da93d0d6ad96f19908ec6", 115 | "grade": false, 116 | "grade_id": "cell-b6862e04967aa07d", 117 | "locked": true, 118 | "points": 1, 119 | "schema_version": 3, 120 | "solution": false, 121 | "task": true 122 | } 123 | }, 124 | "source": [ 125 | "### Question 1 (1 point)\n", 126 | "\n", 127 | "1. Code review: Take turns briefly talking through your code and process (3-5 min), then spend the remaining time discussing the different approaches you may have taken to get to the same end-goal. Compare the types of visuals you included, and the how behind each of them. \n", 128 | "1. For the last 5 minutes on your own, think of a suggestion of something you would've liked to learn in relation to these topics that we didn't cover." 129 | ] 130 | }, 131 | { 132 | "cell_type": "markdown", 133 | "metadata": { 134 | "deletable": false, 135 | "editable": false, 136 | "nbgrader": { 137 | "cell_type": "markdown", 138 | "checksum": "53adb759fcc2e2fb08d8e244e28ee649", 139 | "grade": false, 140 | "grade_id": "cell-f525efff5ae90397", 141 | "locked": true, 142 | "schema_version": 3, 143 | "solution": false, 144 | "task": false 145 | } 146 | }, 147 | "source": [ 148 | "## A5.ab: Advanced plotting in R [20-30 min] TPS\n", 149 | "#### ab.i Understanding R packages, specifically `ggplot2` and `ggpubr`" 150 | ] 151 | }, 152 | { 153 | "cell_type": "markdown", 154 | "metadata": { 155 | "deletable": false, 156 | "editable": false, 157 | "nbgrader": { 158 | "cell_type": "markdown", 159 | "checksum": "d6cb827b895a318d1d20ca737dbb1a51", 160 | "grade": false, 161 | "grade_id": "cell-a78615968ed71492", 162 | "locked": true, 163 | "points": 1, 164 | "schema_version": 3, 165 | "solution": false, 166 | "task": true 167 | } 168 | }, 169 | "source": [ 170 | "## Question 2 (1 point)\n", 171 | "### Installation of `ggpubr`\n", 172 | "Read the following instructions carefully and ask questions whenever you had problem. The wrong configuration might cause unpredictable conflicts in your personal account. \n", 173 | "1. In the login page of your Jupyterhub, **open a new Terminal session**.\n", 174 | "1. To load dependencies: Under bash, run ~\\$ **`module load gcc/6.3.0`**\n", 175 | "1. To enter the R console: Under bash, run ~\\$ **`R`** \n", 176 | "1. To initiate the installation: Under R, run \\> **`install.packages(\"ggpubr\")`** \n", 177 | "1. When asked \"*Would you like to use a personal library instead? (yes/No/cancel)*\", answer **`y`**\n", 178 | "1. When asked \"*Would you like to create a personal library '~/R/x86_64-pc-linux-gnu-library/3.5' to install packages into? (yes/No/cancel)*\", answer **`y`**\n", 179 | "1. When asked \"*--- Please select a CRAN mirror for use in this session ---*\", answer **`1`**\n", 180 | "1. It will ran for a while and create bunch of messages, eventually you should get the system messages ended as:\n", 181 | "\n", 182 | "```\n", 183 | "** building package indices\n", 184 | "** testing if installed package can be loaded\n", 185 | "* DONE (ggpubr)\n", 186 | "The downloaded source packages are in\n", 187 | " '/tmp/RtmpVkLTww/downloaded_packages'\n", 188 | "```\n", 189 | "9. Come back to this homework and test importing the 2 libraries `ggpubr` and `ggplot2`, report any issue if you get error message.\n" 190 | ] 191 | }, 192 | { 193 | "cell_type": "markdown", 194 | "metadata": { 195 | "deletable": false, 196 | "editable": false, 197 | "nbgrader": { 198 | "cell_type": "markdown", 199 | "checksum": "2c544d4b1d78eecc671a19ecb84c1728", 200 | "grade": false, 201 | "grade_id": "cell-a6756d6c61a89b0c", 202 | "locked": true, 203 | "points": 1, 204 | "schema_version": 3, 205 | "solution": false, 206 | "task": true 207 | } 208 | }, 209 | "source": [ 210 | "### Question 3 (1 point)\n", 211 | "\n", 212 | "1. On your own, describe what the distinction is between a package in R vs base R. Why and when would we want to use a package over base R? Give an example in the context of plotting.\n", 213 | "1. On your own, by `ggplot2` or `ggpubr`, create the same data visualization as you did for HW4 Q1 (use the `games.csv` included in the `data` folder with HW5). Note the aspects that are different or similar, and how `ggplot2` and `ggpubr` are easier to use than base R (or perhaps more difficult). Comment the similarities and differences in your script.\n", 214 | "1. Now, spend 5-10 minutes discussing your finding with your partner. Include notes. \n", 215 | "\n", 216 | "_(Hint: a few examples for your idea)_\n", 217 | "\n", 218 | "- (Bonus +2 points in total grades) It's basic to recreate the panel **A** and **B** by `ggplot2` or `ggpubr`, and sufficient to get full credit in this question to generate/improve either **single** one of them with default settings - still try as much as you can to improve it in your own way. However, the panel **C** is an advanced one for students seeking for challenges, which might need more libraries and combined knowledge from previous lecture. Therefore, extra points will be applied to your total grades if achieving the **FULL figure** - including the **3 panels joint together** with proper **customized transparent color**, **font size/style**, **shared legend and axis scale**, **readable labels/titles** and **aspect ratio = 3:1**, **high resolution** output (dpi=300). Note we won't cover the potential solution (build your own coding style!!) but it's common requisites for a formal publication. (WARNING: Revisit the bonus question when you really have plenty of time after finishing this homework...)" 219 | ] 220 | }, 221 | { 222 | "cell_type": "markdown", 223 | "metadata": { 224 | "deletable": false, 225 | "editable": false, 226 | "nbgrader": { 227 | "cell_type": "markdown", 228 | "checksum": "b55a1d0f923ea91e4b04970695357308", 229 | "grade": false, 230 | "grade_id": "cell-9ee29f9bb2dadde5", 231 | "locked": true, 232 | "schema_version": 3, 233 | "solution": false, 234 | "task": false 235 | } 236 | }, 237 | "source": [ 238 | "#### ab.ii Understanding the fundamentals of data visualization (on your own time) " 239 | ] 240 | }, 241 | { 242 | "cell_type": "markdown", 243 | "metadata": { 244 | "deletable": false, 245 | "editable": false, 246 | "nbgrader": { 247 | "cell_type": "markdown", 248 | "checksum": "83a7f8312b5c1e18e89781ebff023fac", 249 | "grade": false, 250 | "grade_id": "cell-276439f2a1dfb63e", 251 | "locked": true, 252 | "points": 1, 253 | "schema_version": 3, 254 | "solution": false, 255 | "task": true 256 | } 257 | }, 258 | "source": [ 259 | "### Question 4 (1 point)\n", 260 | "\n", 261 | "1. Walk through the following lecture and complete the tutorials therein. Use this space to take notes of what you learned
\n", 262 | "https://docs.google.com/presentation/d/1Kyogt2wSJITp5eY9zWJwqCU5gUt0w-8KhniU5dYyunQ/edit?usp=sharing
\n", 263 | "https://sabahzero.github.io/dataviz/resources\n", 264 | "1. Include an enhancement to these fundamentals. What is missing or even out of date for either on the tutorial directly or the Resources page?\n", 265 | "1. Reflections: On an integer scale of `1-5`, `1` being very easy and `5` being the most difficult, where would you rank today's exercises? Provide brief notes on what was easy vs difficult, and why.
\n" 266 | ] 267 | }, 268 | { 269 | "cell_type": "markdown", 270 | "metadata": { 271 | "deletable": false, 272 | "editable": false, 273 | "nbgrader": { 274 | "cell_type": "markdown", 275 | "checksum": "33079602774a9426187610400bd3a2e5", 276 | "grade": false, 277 | "grade_id": "cell-8d9635296d8c05fb", 278 | "locked": true, 279 | "schema_version": 3, 280 | "solution": false, 281 | "task": false 282 | } 283 | }, 284 | "source": [ 285 | "### A5.ba: Visualizing Gene Expression from RNA-Seq Data [20-30 min] Individual\n", 286 | "- Each of the questions are possible to be solved by `tidyverse`" 287 | ] 288 | }, 289 | { 290 | "cell_type": "markdown", 291 | "metadata": { 292 | "deletable": false, 293 | "editable": false, 294 | "nbgrader": { 295 | "cell_type": "markdown", 296 | "checksum": "2c9f7c4c6b020be5cf75c0f5e2990151", 297 | "grade": false, 298 | "grade_id": "cell-5142f94dd21b3d99", 299 | "locked": true, 300 | "points": 1, 301 | "schema_version": 3, 302 | "solution": false, 303 | "task": true 304 | } 305 | }, 306 | "source": [ 307 | "### Question 5 (1 point)\n", 308 | "On your own (10 min)\n", 309 | "1. Load the `data/RNASeq_post-processing.csv` dataset. Explain what the two columns mean in the context of biology and RNA-Seq. Give each of them a header. Include what stage you think it is along the RNA-Seq data analysis pipeline. Additionally, identify where this data came from via NCBI. _(Hint: The dataframe had a few redundant lines needed to be removed.)_\n", 310 | "1. For the next 5 min, discuss with your partner and include notes on updates below.\n", 311 | "\n", 312 | "\n" 313 | ] 314 | }, 315 | { 316 | "cell_type": "markdown", 317 | "metadata": { 318 | "deletable": false, 319 | "editable": false, 320 | "nbgrader": { 321 | "cell_type": "markdown", 322 | "checksum": "f134e90ea2582a45224ad5681dd82216", 323 | "grade": false, 324 | "grade_id": "cell-28f3b1fab0c4be24", 325 | "locked": true, 326 | "points": 1, 327 | "schema_version": 3, 328 | "solution": false, 329 | "task": true 330 | } 331 | }, 332 | "source": [ 333 | "### Question 6 (1 point)\n", 334 | "In the remaining time\n", 335 | "1. Compare expression value of any two genes of interest by boxplot. \n", 336 | "2. How many experiement here included in the dataset? Determine the statistical significance of your target genes.\n", 337 | "3. Come up with a strategy to impute the missing value for statistical test, if necessary.\n", 338 | "\n", 339 | "\n", 340 | "\n", 341 | "\n" 342 | ] 343 | }, 344 | { 345 | "cell_type": "markdown", 346 | "metadata": { 347 | "deletable": false, 348 | "editable": false, 349 | "nbgrader": { 350 | "cell_type": "markdown", 351 | "checksum": "53bfb4f19df25956cccb07f00f928f0d", 352 | "grade": false, 353 | "grade_id": "cell-5a37512931399467", 354 | "locked": true, 355 | "schema_version": 3, 356 | "solution": false, 357 | "task": false 358 | } 359 | }, 360 | "source": [ 361 | "### A5.bb Applying R Skills to Biological Meaning [20-30 min] Individual" 362 | ] 363 | }, 364 | { 365 | "cell_type": "markdown", 366 | "metadata": { 367 | "deletable": false, 368 | "editable": false, 369 | "nbgrader": { 370 | "cell_type": "markdown", 371 | "checksum": "40058811ed2428841c3def3595daff0e", 372 | "grade": false, 373 | "grade_id": "cell-f00556c7b94fc20e", 374 | "locked": true, 375 | "points": 1, 376 | "schema_version": 3, 377 | "solution": false, 378 | "task": true 379 | } 380 | }, 381 | "source": [ 382 | "### Question 7 (1 point)\n", 383 | "1. Create the heatmap for the Q5. \n", 384 | "1. Join these two figures together. _(Hint: consider using `ggpubr` or other packages)_\n", 385 | "\n", 386 | "\n" 387 | ] 388 | }, 389 | { 390 | "cell_type": "markdown", 391 | "metadata": { 392 | "deletable": false, 393 | "editable": false, 394 | "nbgrader": { 395 | "cell_type": "markdown", 396 | "checksum": "7b98556d86a8867907a1b15cc7804be8", 397 | "grade": false, 398 | "grade_id": "cell-702f38e7c5698214", 399 | "locked": true, 400 | "points": 1, 401 | "schema_version": 3, 402 | "solution": false, 403 | "task": true 404 | } 405 | }, 406 | "source": [ 407 | "### Question 8 (1 point)\n", 408 | "Determine the statistical significance of these two figures and and show them in your joined plot. Describe why you chose these statistics, and the specifics of tests involve. Explain what these say about the data. (Hint: to compare 2 genes of interest, you would like to calculate fold change in $log2$-scale and get $p$-value from statistical test)\n", 409 | "\n", 410 | "\n" 411 | ] 412 | }, 413 | { 414 | "cell_type": "markdown", 415 | "metadata": { 416 | "deletable": false, 417 | "editable": false, 418 | "nbgrader": { 419 | "cell_type": "markdown", 420 | "checksum": "07beeafdf07addede2416a69e7c18369", 421 | "grade": false, 422 | "grade_id": "cell-e3ee869194aa985e", 423 | "locked": true, 424 | "points": 1, 425 | "schema_version": 3, 426 | "solution": false, 427 | "task": true 428 | } 429 | }, 430 | "source": [ 431 | "### Question 9 (1 point)\n", 432 | "Create a loop to repeat same analysis process for multiple pairs of genes. Generate figures above with statistics as png files.\n" 433 | ] 434 | }, 435 | { 436 | "cell_type": "markdown", 437 | "metadata": { 438 | "deletable": false, 439 | "editable": false, 440 | "nbgrader": { 441 | "cell_type": "markdown", 442 | "checksum": "e958e7481700b64880f08b4f91d5916e", 443 | "grade": false, 444 | "grade_id": "cell-260b38f4ff73f25d", 445 | "locked": true, 446 | "points": 1, 447 | "schema_version": 3, 448 | "solution": false, 449 | "task": true 450 | } 451 | }, 452 | "source": [ 453 | "### Question 10 (1 point)\n", 454 | "Advanced: Ask another biological question and include a 3rd figure with statistics as one joined image. " 455 | ] 456 | }, 457 | { 458 | "cell_type": "markdown", 459 | "metadata": { 460 | "deletable": false, 461 | "editable": false, 462 | "nbgrader": { 463 | "cell_type": "markdown", 464 | "checksum": "61bb3d70d05fdcb0143ddfd612678f3e", 465 | "grade": false, 466 | "grade_id": "cell-d81ee466e43323f1", 467 | "locked": true, 468 | "points": 1, 469 | "schema_version": 3, 470 | "solution": false, 471 | "task": true 472 | } 473 | }, 474 | "source": [ 475 | "### Question 11 (1 point)\n", 476 | "1. Reflections: On an integer scale of `1-5`, `1` being very easy and `5` being the most difficult, where would you rank the A1.bb assignment and why? Include some notes about what you gained from this past week that you didn't know before as well as notes of things you already knew.\n", 477 | "\n", 478 | "2. Improvements: Notice a [potentially intentional] mistake, or an area of this homework that could have been improved? Include your thoughts here. " 479 | ] 480 | } 481 | ], 482 | "metadata": { 483 | "kernelspec": { 484 | "display_name": "R", 485 | "language": "R", 486 | "name": "ir" 487 | }, 488 | "language_info": { 489 | "codemirror_mode": "r", 490 | "file_extension": ".r", 491 | "mimetype": "text/x-r-source", 492 | "name": "R", 493 | "pygments_lexer": "r", 494 | "version": "3.5.1" 495 | } 496 | }, 497 | "nbformat": 4, 498 | "nbformat_minor": 4 499 | } 500 | -------------------------------------------------------------------------------- /Homework/data/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuLab/Applied-Bioinformatics/7c01300871e64c09fec7ade1af4c2f3c8bb074e5/Homework/data/.DS_Store -------------------------------------------------------------------------------- /Homework/data/art/artists.txt: -------------------------------------------------------------------------------- 1 | KILIAN, Wolfgang (1581-1662) Baroque German graphic artist (Augsburg) 2 | KINSOEN, François-Joseph (1771-1839) Romanticism Flemish painter 3 | KISS, August Karl Edouard (1802-1865) Romanticism German sculptor 4 | KISS, Bálint (1802-1868) Romanticism Hungarian painter (Pest) 5 | KLEINER, Salomon (1703-1761) Baroque German graphic artist 6 | KLENZE, Leo von (1784-1864) Romanticism German architect 7 | KLESECKER, Justus (see GLESKER, Justus) (c. 1615-1678) Baroque German sculptor (Franconia) 8 | KLINGER, Max (1857-1920) Realism German painter 9 | KLOCKER, Hans (active 1478-1500l) Northern Renaissance Austrian sculptor (South Tyrol) 10 | KLODT, Mikhail Konstantinovich (c. 1832-1902) Realism Russian painter (St. Petersburg) 11 | KLODT, Pyotr Karlovich (1805-1867) Romanticism Russian sculptor (St. Petersburg) 12 | TACCA, Ferdinando (1619-c. 1688) Baroque Italian sculptor (Florence) 13 | TACCA, Pietro (1577-1640) Baroque Italian sculptor (Florence) 14 | TACCONE, Paolo (see PAOLO ROMANO) (c. 1415-c. 1470) Early Renaissance Italian sculptor (Rome) 15 | TADDEO DI BARTOLO (1362/63-1422) Medieval Italian painter (Siena) 16 | TADDEO DI FERRARA (see CRIVELLI, Taddeo) (active 1451-c. 1479) Early Renaissance Italian illuminator (Ferrara) 17 | TADOLINI, Scipione (1822-1892) Realism Italian sculptor (Rome) 18 | TALENTI, Francesco (c. 1300-after 1369) Medieval Italian architect (Florence) 19 | TALENTI, Simone (c. 1330-after 1383) Medieval Italian architect (Florence) 20 | TALPA, Bartolo (active c. 1495) Early Renaissance Italian sculptor (Mantua) 21 | TAMAGNI, Vincenzo (1492-1530) High Renaissance Italian painter (San Gimignano) 22 | TAMAGNINO, Antonio (see PORTA, Antonio della) (active 1489–1519) Early Renaissance Italian sculptor 23 | TAMM, Franz Werner von (1658-1724) Baroque German painter 24 | TANZIO DA VARALLO (c. 1580-c. 1632) Baroque Italian painter 25 | TARAVAL, Guillaume-Thomas-Raphaël (1701-1750) Baroque French painter (Stockholm) 26 | TARAVAL, Hugues (1729-1785) Rococo French painter (Paris) 27 | TARAVAL, Louis-Gustave (1738-1794) Neoclassicism French graphic artist 28 | TARBELL, Edmund Charles (1862-1938) Impressionism American painter 29 | TARCHIANI, Filippo (1576-1645) Baroque Italian painter (Florence) 30 | TARDIEU, Nicolas-Henry (1674-1749) Baroque French graphic artist (Paris) 31 | TARGONE, Cesare (active 1575-1590) Mannerism Italian goldsmith 32 | TARSIA, Antonio (c. 1662-1739) Baroque Austrian sculptor (Venice) 33 | TARUFFI, Emilio (1633-1696) Baroque Italian painter (Bologna) 34 | TASSAERT, Jean-Pierre-Antoine (1727-1788) Rococo Flemish sculptor 35 | TASSAERT, Octave (1800-1874) Romanticism French painter 36 | TASSEL, Jean (1608-1667) Baroque French painter (Langres) 37 | TASSI, Agostino (1578-1644) Baroque Italian painter (Rome) 38 | TAUNAY, Nicolas Antoine (1755-1830) Rococo French painter 39 | TEDESCO, Carlo (see SFERINI, Carlo Leopoldo) (1652-1698) Baroque Italian painter (Verona) 40 | TEDESCO, Giovanni Paolo (see SCHOR, Johann Paul) (1615-1674) Baroque Italian painter (Rome) 41 | TEERLINC, Levina c. 1515-1576) Mannerism Flemish miniaturist (London) 42 | TELEPY, Károly (1828-1906) Romanticism Hungarian painter 43 | TEMANZA, Tommaso (1705-1789) Rococo Italian architect (Venice) 44 | TEMPEL, Abraham van den (1622/23-1672) Baroque Dutch painter (Amsterdam) 45 | TEMPESTA, Antonio (1555-1630) Baroque Italian painter (Florence) 46 | TEMPESTA, Pietro (see MULIER, Pieter the Younger) (1637-1701) Baroque Dutch painter (Italy) 47 | TENERANI, Pietro (1789-1869) Neoclassicism Italian sculptor 48 | TENGNAGEL, Jan (1584-1635) Baroque Dutch painter (Amsterdam) 49 | TENIERS, Abraham (1629-1670) Baroque Flemish painter (Antwerp) 50 | TENIERS, David the Elder (1582-1649) Baroque Flemish painter (Antwerp) 51 | TENIERS, David the Younger (1610-1690) Baroque Flemish painter (Antwerp) 52 | TERBORCH, Gerard (1617-1681) Baroque Dutch painter (Deventer) 53 | TERBRUGGHEN, Hendrick (1588-1629) Baroque Dutch painter (Utrecht) 54 | TERILLI, Francesco (active 1610-1630) Baroque Italian sculptor (Feltre) 55 | TERRENI, Giuseppe Maria (1739-1811) Neoclassicism Italian painter (Livorno) 56 | TERZIO, Francesco (c. 1523-1591) Mannerism Italian painter (Vienna) 57 | TESSIN, Nicodemus the Elder (1615-1681) Baroque Swedish architect (Stockholm) 58 | TESSIN, Nicodemus the Younger (1654-1728) Baroque Swedish architect (Stockholm) 59 | TESTA, Pietro (1611-1650) Baroque Italian painter (Rome) 60 | TESTELIN, Henri (1616-1695) Baroque French painter 61 | TETRODE, Willem Danielsz van (c. 1525-c. 1587) Mannerism Netherlandish sculptor 62 | KNEBEL, Franz (1809-1877) Romanticism Swiss painter (Rome) 63 | KNELLER, Sir Godfrey (1646-1723) Baroque English painter 64 | KNIJFF, Jacob (1639-1681) Baroque Dutch painter (London) 65 | KNIJFF, Wouter (c. 1607-after 1693) Baroque Dutch painter (Haarlem) 66 | KNIP, Henriëtte (1821-1909) Realism Dutch painter (Brussels) 67 | KNIP, Henriëtte Geertruida (1783-1842) Romanticism Dutch painter 68 | KNIP, Josephus Augustus (1777-1847) Romanticism Dutch painter 69 | KNIP, Mattheus Derk (1785-1845) Romanticism Dutch painter 70 | KNIP, Nicolaas Frederik (1741-1808) Rococo Dutch painter 71 | KNOBELSDORFF, Georg Wenceslaus von (1699-1753) Baroque German architect (Berlin) 72 | KNOLLER, Martin (1725-1804) Neoclassicism Austrian painter (Italy) 73 | KNÜPFER, Nicolaus (c. 1603-1655) Baroque Dutch painter 74 | KNYFF, Jacob (see KNIJFF, Jacob) (1639-1681) Baroque Dutch painter (London) 75 | KNYFF, Wouter (see KNIJFF, Wouter) (c. 1607-after 1693) Baroque Dutch painter (Haarlem) 76 | KOBELL, Franz (1749-1822) Rococo German painter (Munich) 77 | KOBELL, Hendrik (1751-1779) Rococo Dutch painter (Rotterdam) 78 | KOBELL, Jan I (1755-1833) Rococo Dutch graphic artist (Rotterdam) 79 | KOBELL, Jan II (1778-1814) Neoclassicism Dutch painter 80 | KOBELL, Wilhelm von (1766-1853) Romanticism German painter 81 | KOBERGER, Anton (c. 1440-1513) Northern Renaissance German graphic artist (Nuremberg) 82 | KŘBKE, Christen (1810-1848) Romanticism Danish painter 83 | KOCH, Joseph Anton (1768-1839) Romanticism Austrian painter 84 | KOEBERGER, Wenzel (see COBERGHER, Wenceslas) (c. 1560-1634) Baroque Flemish architect 85 | KOEDIJCK, Isaack (c. 1617-c. 1668) Baroque Dutch painter (Amsterdam) 86 | KOEKKOEK, Barend Cornelis (1803-1862) Romanticism Dutch painter 87 | KOERBECKE, Johann (c. 1420-1490) Northern Renaissance German painter (Münster) 88 | KOETS, Roelof (c. 1592-1655) Baroque Dutch painter (Haarlem) 89 | KOKORINOV, Alexander Filippovich (1726-1772) Baroque Russian architect (St. Petersburg) 90 | KOLBE, Carl Wilhelm (1759-1835) Neoclassicism German painter 91 | KOLLONITSCH, Christian (1730-1802) Rococo Austrian painter (Vienna) 92 | KOLUNIĆ, Martin (see ROTA, Martino) (c. 1520-1583) Mannerism Other painter (Vienna) 93 | KOMPE, Jan ten (see COMPE, Jan ten) (1713-1761) Baroque Dutch painter (Amsterdam) 94 | KÖNIG, Johann (1586-1642) Baroque German painter (Augsburg) 95 | KONINCK, Daniël de (1668-after 1720) Baroque Dutch painter (London) 96 | KONINCK, David de (see CONINCK, David de) (c. 1644-c. 1701) Baroque Flemish painter 97 | KONINCK, Philips (1619-1688) Baroque Dutch painter (Amsterdam) 98 | KONINCK, Salomon (1609-1656) Baroque Dutch painter (Amsterdam) 99 | KONRAD von Soest (active 1394-1422) Northern Renaissance German painter (Westphalie) 100 | KOPISCH, August (1799-1853) Romanticism German painter (Berlin) 101 | AACHEN, Hans von (1552-1615) Mannerism German painter 102 | AAGAARD, Carl Frederik (1833-1895) Realism Danish painter (Copenhagen) 103 | ABADIA, Juan de la (active 1470-1490) Early Renaissance Spanish painter (Huesca) 104 | ABAQUESNE, Masséot (c 1500-1564) High Renaissance French potter 105 | ABBATE, Niccolò dell' (1509-1571) Mannerism Italian painter (Bologna) 106 | ABBATI, Giuseppe (1836-1868) Realism Italian painter 107 | ABBATINI, Guido Ubaldo (c. 1602-1656) Baroque Italian painter (Rome) 108 | ABBONDI, Antonio di Pietro (see SCARPAGNINO) (c. 1465-1549) High Renaissance Italian architect (Venice) 109 | ABEELE, Pieter van (1608-1684) Baroque Dutch sculptor (Amsterdam) 110 | ABILDGAARD, Nicolai (1743-1809) Romanticism Danish painter 111 | ABONDIO, Antonio (1538-1591) Mannerism Italian sculptor (Vienna) 112 | ACERO Y AREBO, Vicente (c. 1677-1739) Baroque Spanish architect 113 | ACHENBACH, Oswald (1827-1905) Realism German painter (Dusseldorf) 114 | ADAM, Albrecht (1786-1862) Romanticism German painter (Munich) 115 | ADAM, Lambert-Sigisbert (1700-1759) Baroque French sculptor (Nancy) 116 | ADAM, Nicolas-Sébastien (1705-1778) Baroque French sculptor (Nancy) 117 | ADAM, Robert (1728-1792) Baroque Scottish architect (London) 118 | ADAM-SALOMON, Antoine-Samuel (1818-1881) Realism French sculptor (Paris) 119 | ADELCRANTZ, Carl Fredrik (1716-1796) Neoclassicism Swedish architect 120 | ADEMOLLO, Luigi (1764-1849) Neoclassicism Italian painter (Florence) 121 | ADLER, Salomon (1630-1709) Baroque German painter (Milan) 122 | ADOLFZOON, Christoph (see ADOLPHI, Christoffel) (c. 1631-1680) Baroque Dutch sculptor (Amsterdam) 123 | ADOLPHI, Christoffel (c. 1631-1680) Baroque Dutch sculptor (Amsterdam) 124 | ADRIAEN VAN UTRECHT (see UTRECHT, Adriaen van) (1599-1652) Baroque Flemish painter 125 | ADRIAENSSEN, Alexander (1587-1661) Baroque Flemish painter (Antwerp) 126 | ADRIANO FIORENTINO (ca. 1455-1499) Early Renaissance Italian sculptor (Florence) 127 | AELST, Willem van (1627-c. 1683) Baroque Dutch painter (Delft) 128 | AENVANCK, Theodoor (1633-1690) Baroque Flemish painter (Antwerp) 129 | AERT VAN ORT (active 1490-1536) Northern Renaissance Flemish glass painter 130 | AERTSEN, Pieter (1508-1575) Northern Renaissance Netherlandish painter (Amsterdam) 131 | AGASSE, Jacques-Laurent (1767-1849) Neoclassicism Swiss painter (London) 132 | AGNOLO DA SIENA (see AGNOLO DI VENTURA) (active 1311-1349) Medieval Italian sculptor (Siena) 133 | AGNOLO DI POLO (c. 1470-after 1498) Early Renaissance Italian sculptor (Florence) 134 | AGNOLO DI VENTURA (active 1311-1349) Medieval Italian sculptor (Siena) 135 | AGOSTINO DI DUCCIO (1418-1481) Early Renaissance Italian sculptor (Rimini) 136 | AGOSTINO DI GIOVANNI (active 1310-1347) Medieval Italian sculptor (Siena) 137 | AGOSTINO VENEZIANO (see MUSI, Agostino dei) (c. 1490-c. 1536) High Renaissance Italian graphic artist 138 | AGRATE, Gian Francesco Ferrari d' (1489-c. 1563) High Renaissance Italian sculptor (Parma) 139 | AGUADO LÓPEZ, Antonio (1764-1831) Neoclassicism Spanish architect (Madrid) 140 | AIVAZOVSKY, Ivan Konstantinovich (1817-1900) Realism Russian painter 141 | AKEN, Joseph van (c. 1699-1749) Rococo Flemish painter (London) 142 | AKOTANTOS, Angelos (?-c. 1457) Medieval Greek painter (Crete) 143 | ALBA, Macrino d' (c. 1460-c. 1528) Early Renaissance Italian painter (Alba) 144 | ALBANI, Francesco (1578-1660) Baroque Italian painter (Bologna) 145 | ALBEREGNO, Jacobello (died before1397) Medieval Italian painter (Venice) 146 | ALBERTI, Antonio (c. 1390-c. 1442) Early Renaissance Italian painter (Urbino) 147 | ALBERTI, Cherubino (1553-1615) Mannerism Italian painter (Rome) 148 | ALBERTI, Giovanni (1558-1601) Mannerism Italian painter (Rome) 149 | ALBERTI, Leon Battista (1404-1472) Early Renaissance Italian architect 150 | ALBERTINELLI, Mariotto (1474-1515) Early Renaissance Italian painter (Florence) 151 | -------------------------------------------------------------------------------- /Homework/data/fastq/simulated1.R1.fq: -------------------------------------------------------------------------------- 1 | @Puerto_5207_5777_1:0:0_2:0:0_0/1 2 | TGGGAAAACCAGGAGAGTTCTTCCTGAAATAGTCCGTGAAGCCATAAAAAGAAGACTCCGTACTGTGATC 3 | + 4 | 2222222222222222222222222222222222222222222222222222222222222@@@@@@@@@ 5 | @Puerto_4126_4595_1:0:0_0:0:0_1/1 6 | ACTTACCATTTGTCATGGCCCTGGGACTAACCGCTGTGAGGCTGGTCGACCCGATCAACGTGGTGGGACT 7 | + 8 | 2222222222222222222222222222222222222222222222222222222222222222222222 9 | @Puerto_8069_8649_4:0:0_1:0:0_2/1 10 | GCCAGACAACCCCGTTTATTAGAGAGGACGCTGACCCTTGTGTGGGGGCCTCATAGCTTCCATGGTAAGC 11 | + 12 | 2222222222222222222222222222222222222222222222222222222222222222222222 13 | @Puerto_2090_2540_1:0:0_3:0:0_3/1 14 | CTCTAAGCTGATGCTGGAACTTGATCCACCATTTGGGGACTCTTACATTGTCATAGGAGTCGGGGAGAAG 15 | + 16 | 2222222222222222222222222222222222222222222222222222222222222222222222 17 | @Puerto_7758_8266_0:0:0_1:0:0_4/1 18 | GGCATCACCGAGGTGTGCAGAGAAGAGGCCCGCCGCGCCCTCAAGGACGGTGTGGCAACGGGAGGCCATG 19 | + 20 | 2222222222222222222222222222222222222222222222222222222222222222222222 21 | @Puerto_2795_3256_2:0:0_0:0:0_5/1 22 | GAGATTGCCCGTGCCTGTGAACGAGCTGCCCCACGGGTGGAAGGCTTTGGGGAAATCGTATTTCGTCAGA 23 | + 24 | 2222222222222222222222222222222222222222222222222222222222222222222222 25 | @Puerto_2172_2650_0:0:0_2:0:0_6/1 26 | ATACCATCATCCCAGGCTTGCTTGACTGCTGCTGGCAATCTACGGGGGGAGTCAGGATGGTACTTGTACC 27 | + 28 | 2222222222222222222222222222222222222222222222222222222222222222222222 29 | @Puerto_3618_4126_1:0:0_1:0:0_7/1 30 | TTCTTCTTCACACTGCCTTTTCCCTTCAGAGAGAGGAGCAAAAACCCCCCGCAAGTAGCAAGGCCTGCTC 31 | + 32 | 2222222222222222222222222222222222222222222222222222222222222222222222 33 | @Puerto_362_896_1:0:0_1:0:0_8/1 34 | GAAAGATCTGGCTGCCAAGCTGAGAATAATCAATGCTAGGAAGGAGAAGAAGAGACGAGGCGCAGATACT 35 | + 36 | 2222222222222222222222222222222222222222222222222222222222222222222222 37 | @Puerto_8730_9289_0:0:0_1:0:0_9/1 38 | GTTTTCAAGGAAAAAGTGGACACTAGGGTGCCAGACCCCCAAGAAGGCACTCGTCAGGTTATGAGCATGG 39 | + 40 | 2222222222222222222222222222222222222222222222222222222222222222222222 41 | @Puerto_2020_2513_1:0:0_2:0:0_a/1 42 | ACATGCAAACTCTGACCCCAGTTGGGAGGTTGATAACCGCTAACCCCGTACTCACTGAAAGCACTGAGAA 43 | + 44 | 2222222222222222222222222222222222222222222222222222222222222222222222 45 | @Puerto_8179_8741_1:0:0_0:0:0_b/1 46 | GGCTTGAAAAAAGACCAGGAGCCTTTTGTATAAAAGTGTTGTGCCCATACACCAGCACTATGCTGGAAAC 47 | + 48 | 2222222222222222222222222222222222222222222222222222222222222222222222 49 | @Puerto_8541_9051_1:0:0_2:0:0_c/1 50 | TCTTTTCTCTTTTTCCCATCATGTTGTACACACAGCTCTGGCACTCTCCTCTCAGGTGGTGCACTCTTTG 51 | + 52 | 2222222222222222222222222222222222222222222222222222222222222222222222 53 | @Puerto_1817_2345_0:0:0_3:0:0_d/1 54 | CACTGATTTGAAAGGTGCTCCAAAAATTTGATGGATGCGCTTGCCCAATGAGTTGAGAGCGCCTCCAACT 55 | + 56 | 2222222222222222222222222222222222222222222222222222222222222222222222 57 | @Puerto_8936_9483_0:0:0_1:0:0_e/1 58 | CTTTTCCGCTCCCCCTTTGGTCTTGTCTCGAAATAATGTCCATAACTGTTTTCCCTTTTTCAGCTGGTCT 59 | + 60 | 2222222222222222222222222222222222222222222222222222222222222222222222 61 | @Puerto_1548_2094_1:0:0_2:0:0_f/1 62 | TAGAGTTCTCAGTTCTTTCAGTGATTACGGGGTTAGCTGTTATCAACCTCCCAACTGGGGTCAGAGTTTG 63 | + 64 | 2222222222222222222222222222222222222222222222222222222222222222222222 65 | @Puerto_7508_8051_2:0:0_2:0:0_10/1 66 | ACTCTTAATACGGACTATGATCCACCCATAGCTTTGCACCAACACGGGTTCTTCATGACCAGGGCCTCCT 67 | + 68 | 2222222222222222222222222222222222222222222222222222222222222222222222 69 | @Puerto_6768_7305_1:0:0_0:0:0_11/1 70 | CCAGCCAGAATTGCATGTGTCCACATTGTTGTGTTCCTATTGCTGGTGGTGCTCATACCTGAGCCAGAAA 71 | + 72 | 2222222222222222222222222222222222222222222222222222222222222222222222 73 | @Puerto_5435_5937_5:0:0_1:0:0_12/1 74 | GAATGACTCTCTCGCCATCAAGAATGACCGGCTTTAGGCATCTCCTGGAATCTATGACACGGTCAGCTTT 75 | + 76 | @@@2222222222222222222222222222222222222222222222222222222222222222222 77 | @Puerto_9144_9685_4:0:0_0:0:0_13/1 78 | TTGAACGAGGATCACTGGATGTGGAGATAGAACACAGGAGGTGGTGTTTAAGGGCTGGGATTACAAAGAC 79 | + 80 | 2222222222222222222222222222222222222222222222222222222222222222222222 81 | -------------------------------------------------------------------------------- /Homework/data/fastq/simulated1.R2.fq: -------------------------------------------------------------------------------- 1 | @Puerto_5207_5777_1:0:0_2:0:0_0/2 2 | TCTGCTGAGCTGTCTGACCCGTTTTCCAGCCTTTGTCCGACAAGCTGCGATCTCATTGCCGTTCCTCACG 3 | + 4 | 2222222222222222222222222222222222222222222222222222222222222222222222 5 | @Puerto_4126_4595_1:0:0_0:0:0_1/2 6 | GTATACGTACCACGCTCCAGCTGCAAAGGGTATGGCTATTGGGTTCATGCCACAGATGGTCATCAGGACC 7 | + 8 | 2222222222222222222222222222222222222222222222222222222222222222222222 9 | @Puerto_8069_8649_4:0:0_1:0:0_2/2 10 | TATGGCGGCTGAGCCGTGTGACAGGTTGCTGTGTGACCTAGGTGAGTCATCAACTAGTCCTGCAGTGGAA 11 | + 12 | 2222222222222222222222222222222222222222222222222222222222222222222222 13 | @Puerto_2090_2540_1:0:0_3:0:0_3/2 14 | TGTACCGCATCTCGACTCCTTCTTTGAGAAGTCCACCGATCACCCCACATCAGCAGAGCCGGCTGTGGAT 15 | + 16 | 2222222222222222222222222222222222222222222222222222222222222222222222 17 | @Puerto_7758_8266_0:0:0_1:0:0_4/2 18 | CGCTGCAGTCGCTCCAGGGTTTCCATGATAGTGCTGGTGTATGGGCACAACACTTTTATACAAAAGGCTC 19 | + 20 | 2222222222222222222222222222222222222222222222222222222222222222222222 21 | @Puerto_2795_3256_2:0:0_0:0:0_5/2 22 | GTATTGTGATGGCTGAGTGGCCCAGCTAAAGACTTGGGTATGATCAGATCACTCTCTTCTATTCCATCTG 23 | + 24 | 2222222222222222222222222222222222222222222222222222222222222222222222 25 | @Puerto_2172_2650_0:0:0_2:0:0_6/2 26 | CACTGGCACAGGAGTGGCAGCACCATTGGAAAAGCATTTGAAGCCACTGTGAGAGGTGCCAAGAGAATGG 27 | + 28 | 2222222222222222222222222222222222222222222222222222222222222222222222 29 | @Puerto_3618_4126_1:0:0_1:0:0_7/2 30 | AAGAAGAGAATGACCACAAAGATCATGATAAGCACATCAATGGCAGTGCTGGTAGCTATGATCCTGGGAG 31 | + 32 | 2222222222222222222222222222222222222222222222222222222222222222222222 33 | @Puerto_362_896_1:0:0_1:0:0_8/2 34 | GGCAGCTGCTGCTAACGCGAAGCCAGGGTTCCTGAATATCCAATTTTCGACTCTAATCAAGTGGTTTGTG 35 | + 36 | 2222222222222222222222222222222222222222222222222222222222222222222222 37 | @Puerto_8730_9289_0:0:0_1:0:0_9/2 38 | GTGTCCCAGCCAGCAGTGTCATCTGCATACATCCTTCCTCCTGGTATACGACTCATCTGTTCTAGGACAT 39 | + 40 | 2222222222222222222222222222222222222222222222222222222222222222222222 41 | @Puerto_2020_2513_1:0:0_2:0:0_a/2 42 | GACGTGCACCGAGCACCCCACATCAGCAGAGACGGCTGTGGATAAGAAGATCAACACTCCCCCTAAGGCC 43 | + 44 | 2222222222222222222222222222222222222222222222222222222222222222222222 45 | @Puerto_8179_8741_1:0:0_0:0:0_b/2 46 | TTCCTTGAAAACTCTTTGCTGACCATACGGTGTGGTGTCGGTCATGGCTATTCCTGTGACTCCAGTCACC 47 | + 48 | 2222222222222222222222222222222222222222222222222222222222222222222222 49 | @Puerto_8541_9051_1:0:0_2:0:0_c/2 50 | ACGTGGTTCTTTGACGAGAACCACCCATATAGGACATGGGCTTACCATGGAAGCTATGAGGCCCCCAGAC 51 | + 52 | 2222222222222222222222222222222222222222222222222222222222222222222222 53 | @Puerto_1817_2345_0:0:0_3:0:0_d/2 54 | AAAGGGAAGGCTGTCCTCTGGCCACTTGAAATGTCGCCTGAAAATGGATAAACTTAGATTGAAGGGCGTG 55 | + 56 | 2222222222222222222222222222222222222222222222222222222222222222222222 57 | @Puerto_8936_9483_0:0:0_1:0:0_e/2 58 | AGTGGAAGCTGTGAACGATCCAAGGTTCTGGGCTCTAGTGGACAAGGAAAGAGAGCACCACCTGAGAGGA 59 | + 60 | 2222222222222222222222222222222222222222222222222222222222222222222222 61 | @Puerto_1548_2094_1:0:0_2:0:0_f/2 62 | GAACGGAGGACAGGCCTTGACTTTTCAGATTTGTATTACTTGACTATGAATAACAAGCACTGGTTGGTTC 63 | + 64 | 2222222222222222222222222222222222222222222222222222222222222222222222 65 | @Puerto_7508_8051_2:0:0_2:0:0_10/2 66 | GATCACAGCCGCAACTTCCACTTTTTGGGCAGGCTCTCCGAACAAGTACTGGAACTCCTCTACAGCCACT 67 | + 68 | 2222222222222222222222222222222222222222222222222222222222222222222222 69 | @Puerto_6768_7305_1:0:0_0:0:0_11/2 70 | CTGCTGCCTGCAGCCCTGGGATCAAGTACATGTAGTGCGCCACGAGCAAAATGATGGCCACTATTAGGGT 71 | + 72 | 2222222222222222222222222222222222222222222222222222222222222222222222 73 | @Puerto_5435_5937_5:0:0_1:0:0_12/2 74 | CAGAGTCCCCCACTATACACTGTATATTATGGATGAGGCCCACTTCACAGATCCCTCAATTCTAGCAGCA 75 | + 76 | 2222222222222222222222222222222222222222222222222222222222222222222222 77 | @Puerto_9144_9685_4:0:0_0:0:0_13/2 78 | TCAATTGGCTTCACAACGCAATCATCTCCACTGACTGCCATTCGTTTGAGCCTATCCCATCCGTTGCTCT 79 | + 80 | 2222222222222222222222222222222222222222222222222222222222222222222222 81 | -------------------------------------------------------------------------------- /Homework/data/fastq/simulated2.R1.fq: -------------------------------------------------------------------------------- 1 | @Puerto_5207_5777_1:0:0_2:0:0_0/1 2 | TGGGAAAACCAGGAGAGTTCTTCCTGAAATAGTCCGTGAAGCCATAAAAAGAAGACTCCGTACTGTGATC 3 | + 4 | 2222222222222222222222222222222222222222222222222222222222222222222222 5 | @Puerto_4126_4595_1:0:0_0:0:0_1/1 6 | ACTTACCATTTGTCATGGCCCTGGGACTAACCGCTGTGAGGCTGGTCGACCCGATCAACGTGGTGGGACT 7 | + 8 | 2222222222222222222222222222222222222222222222222222222222222222222222 9 | @Puerto_8069_8649_4:0:0_1:0:0_2/1 10 | GCCAGACAACCCCGTTTATTAGAGAGGACGCTGACCCTTGTGTGGGGGCCTCATAGCTTCCATGGTAAGC 11 | + 12 | 2222222222222222222222222222222222222222222222222222222222222222222222 13 | @Puerto_2090_2540_1:0:0_3:0:0_3/1 14 | CTCTAAGCTGATGCTGGAACTTGATCCACCATTTGGGGACTCTTACATTGTCATAGGAGTCGGGGAGAAG 15 | + 16 | 2222222222222222222222222222222222222222222222222222222222222222222222 17 | @Puerto_7758_8266_0:0:0_1:0:0_4/1 18 | GGCATCACCGAGGTGTGCAGAGAAGAGGCCCGCCGCGCCCTCAAGGACGGTGTGGCAACGGGAGGCCATG 19 | + 20 | 2222222222222222222222222222222222222222222222222222222222222222222222 21 | @Puerto_2795_3256_2:0:0_0:0:0_5/1 22 | GAGATTGCCCGTGCCTGTGAACGAGCTGCCCCACGGGTGGAAGGCTTTGGGGAAATCGTATTTCGTCAGA 23 | + 24 | 2222222222222222222222222222222222222222222222222222222222222222222222 25 | @Puerto_2172_2650_0:0:0_2:0:0_6/1 26 | ATACCATCATCCCAGGCTTGCTTGACTGCTGCTGGCAATCTACGGGGGGAGTCAGGATGGTACTTGTACC 27 | + 28 | 2222222222222222222222222222222222222222222222222222222222222222222222 29 | @Puerto_3618_4126_1:0:0_1:0:0_7/1 30 | TTCTTCTTCACACTGCCTTTTCCCTTCAGAGAGAGGAGCAAAAACCCCCCGCAAGTAGCAAGGCCTGCTC 31 | + 32 | 2222222222222222222222222222222222222222222222222222222222222222222222 33 | @Puerto_362_896_1:0:0_1:0:0_8/1 34 | GAAAGATCTGGCTGCCAAGCTGAGAATAATCAATGCTAGGAAGGAGAAGAAGAGACGAGGCGCAGATACT 35 | + 36 | 2222222222222222222222222222222222222222222222222222222222222222222222 37 | @Puerto_8730_9289_0:0:0_1:0:0_9/1 38 | GTTTTCAAGGAAAAAGTGGACACTAGGGTGCCAGACCCCCAAGAAGGCACTCGTCAGGTTATGAGCATGG 39 | + 40 | 2222222222222222222222222222222222222222222222222222222222222222222222 41 | @Puerto_2020_2513_1:0:0_2:0:0_a/1 42 | ACATGCAAACTCTGACCCCAGTTGGGAGGTTGATAACCGCTAACCCCGTACTCACTGAAAGCACTGAGAA 43 | + 44 | 2222222222222222222222222222222222222222222222222222222222222222222222 45 | @Puerto_8179_8741_1:0:0_0:0:0_b/1 46 | GGCTTGAAAAAAGACCAGGAGCCTTTTGTATAAAAGTGTTGTGCCCATACACCAGCACTATGCTGGAAAC 47 | + 48 | 2222222222222222222222222222222222222222222222222222222222222222222222 49 | @Puerto_8541_9051_1:0:0_2:0:0_c/1 50 | TCTTTTCTCTTTTTCCCATCATGTTGTACACACAGCTCTGGCACTCTCCTCTCAGGTGGTGCACTCTTTG 51 | + 52 | 2222222222222222222222222222222222222222222222222222222222222222222222 53 | @Puerto_1817_2345_0:0:0_3:0:0_d/1 54 | CACTGATTTGAAAGGTGCTCCAAAAATTTGATGGATGCGCTTGCCCAATGAGTTGAGAGCGCCTCCAACT 55 | + 56 | 2222222222222222222222222222222222222222222222222222222222222222222222 57 | @Puerto_8936_9483_0:0:0_1:0:0_e/1 58 | CTTTTCCGCTCCCCCTTTGGTCTTGTCTCGAAATAATGTCCATAACTGTTTTCCCTTTTTCAGCTGGTCT 59 | + 60 | 2222222222222222222222222222222222222222222222222222222222222222222222 61 | @Puerto_1548_2094_1:0:0_2:0:0_f/1 62 | TAGAGTTCTCAGTTCTTTCAGTGATTACGGGGTTAGCTGTTATCAACCTCCCAACTGGGGTCAGAGTTTG 63 | + 64 | 2222222222222222222222222222222222222222222222222222222222222222222222 65 | @Puerto_7508_8051_2:0:0_2:0:0_10/1 66 | ACTCTTAATACGGACTATGATCCACCCATAGCTTTGCACCAACACGGGTTCTTCATGACCAGGGCCTCCT 67 | + 68 | 2222222222222222222222222222222222222222222222222222222222222222222222 69 | @Puerto_6768_7305_1:0:0_0:0:0_11/1 70 | CCAGCCAGAATTGCATGTGTCCACATTGTTGTGTTCCTATTGCTGGTGGTGCTCATACCTGAGCCAGAAA 71 | + 72 | 2222222222222222222222222222222222222222222222222222222222222222222222 73 | @Puerto_5435_5937_5:0:0_1:0:0_12/1 74 | GAATGACTCTCTCGCCATCAAGAATGACCGGCTTTAGGCATCTCCTGGAATCTATGACACGGTCAGCTTT 75 | + 76 | 2222222222222222222222222222222222222222222222222222222222222222222222 77 | @Puerto_9144_9685_4:0:0_0:0:0_13/1 78 | TTGAACGAGGATCACTGGATGTGGAGATAGAACACAGGAGGTGGTGTTTAAGGGCTGGGATTACAAAGAC 79 | + 80 | 2222222222222222222222222222222222222222222222222222222222222222222222 81 | -------------------------------------------------------------------------------- /Homework/data/fastq/simulated2.R2.fq: -------------------------------------------------------------------------------- 1 | @Puerto_5207_5777_1:0:0_2:0:0_0/2 2 | TCTGCTGAGCTGTCTGACCCGTTTTCCAGCCTTTGTCCGACAAGCTGCGATCTCATTGCCGTTCCTCACG 3 | + 4 | 2222222222222222222222222222222222222222222222222222222222222222222222 5 | @Puerto_4126_4595_1:0:0_0:0:0_1/2 6 | GTATACGTACCACGCTCCAGCTGCAAAGGGTATGGCTATTGGGTTCATGCCACAGATGGTCATCAGGACC 7 | + 8 | 2222222222222222222222222222222222222222222222222222222222222222222222 9 | @Puerto_8069_8649_4:0:0_1:0:0_2/2 10 | TATGGCGGCTGAGCCGTGTGACAGGTTGCTGTGTGACCTAGGTGAGTCATCAACTAGTCCTGCAGTGGAA 11 | + 12 | 2222222222222222222222222222222222222222222222222222222222222222222222 13 | @Puerto_2090_2540_1:0:0_3:0:0_3/2 14 | TGTACCGCATCTCGACTCCTTCTTTGAGAAGTCCACCGATCACCCCACATCAGCAGAGCCGGCTGTGGAT 15 | + 16 | 2222222222222222222222222222222222222222222222222222222222222222222222 17 | @Puerto_7758_8266_0:0:0_1:0:0_4/2 18 | CGCTGCAGTCGCTCCAGGGTTTCCATGATAGTGCTGGTGTATGGGCACAACACTTTTATACAAAAGGCTC 19 | + 20 | 2222222222222222222222222222222222222222222222222222222222222222222222 21 | @Puerto_2795_3256_2:0:0_0:0:0_5/2 22 | GTATTGTGATGGCTGAGTGGCCCAGCTAAAGACTTGGGTATGATCAGATCACTCTCTTCTATTCCATCTG 23 | + 24 | 2222222222222222222222222222222222222222222222222222222222222222222222 25 | @Puerto_2172_2650_0:0:0_2:0:0_6/2 26 | CACTGGCACAGGAGTGGCAGCACCATTGGAAAAGCATTTGAAGCCACTGTGAGAGGTGCCAAGAGAATGG 27 | + 28 | 2222222222222222222222222222222222222222222222222222222222222222222222 29 | @Puerto_3618_4126_1:0:0_1:0:0_7/2 30 | AAGAAGAGAATGACCACAAAGATCATGATAAGCACATCAATGGCAGTGCTGGTAGCTATGATCCTGGGAG 31 | + 32 | 2222222222222222222222222222222222222222222222222222222222222222222222 33 | @Puerto_362_896_1:0:0_1:0:0_8/2 34 | GGCAGCTGCTGCTAACGCGAAGCCAGGGTTCCTGAATATCCAATTTTCGACTCTAATCAAGTGGTTTGTG 35 | + 36 | 2222222222222222222222222222222222222222222222222222222222222222222222 37 | @Puerto_8730_9289_0:0:0_1:0:0_9/2 38 | GTGTCCCAGCCAGCAGTGTCATCTGCATACATCCTTCCTCCTGGTATACGACTCATCTGTTCTAGGACAT 39 | + 40 | 2222222222222222222222222222222222222222222222222222222222222222222222 41 | @Puerto_2020_2513_1:0:0_2:0:0_a/2 42 | GACGTGCACCGAGCACCCCACATCAGCAGAGACGGCTGTGGATAAGAAGATCAACACTCCCCCTAAGGCC 43 | + 44 | 2222222222222222222222222222222222222222222222222222222222222222222222 45 | @Puerto_8179_8741_1:0:0_0:0:0_b/2 46 | TTCCTTGAAAACTCTTTGCTGACCATACGGTGTGGTGTCGGTCATGGCTATTCCTGTGACTCCAGTCACC 47 | + 48 | 2222222222222222222222222222222222222222222222222222222222222222222222 49 | @Puerto_8541_9051_1:0:0_2:0:0_c/2 50 | ACGTGGTTCTTTGACGAGAACCACCCATATAGGACATGGGCTTACCATGGAAGCTATGAGGCCCCCAGAC 51 | + 52 | 2222222222222222222222222222222222222222222222222222222222222222222222 53 | @Puerto_1817_2345_0:0:0_3:0:0_d/2 54 | AAAGGGAAGGCTGTCCTCTGGCCACTTGAAATGTCGCCTGAAAATGGATAAACTTAGATTGAAGGGCGTG 55 | + 56 | 2222222222222222222222222222222222222222222222222222222222222222222222 57 | @Puerto_8936_9483_0:0:0_1:0:0_e/2 58 | AGTGGAAGCTGTGAACGATCCAAGGTTCTGGGCTCTAGTGGACAAGGAAAGAGAGCACCACCTGAGAGGA 59 | + 60 | 2222222222222222222222222222222222222222222222222222222222222222222222 61 | @Puerto_1548_2094_1:0:0_2:0:0_f/2 62 | GAACGGAGGACAGGCCTTGACTTTTCAGATTTGTATTACTTGACTATGAATAACAAGCACTGGTTGGTTC 63 | + 64 | 2222222222222222222222222222222222222222222222222222222222222222222222 65 | @Puerto_7508_8051_2:0:0_2:0:0_10/2 66 | GATCACAGCCGCAACTTCCACTTTTTGGGCAGGCTCTCCGAACAAGTACTGGAACTCCTCTACAGCCACT 67 | + 68 | 2222222222222222222222222222222222222222222222222222222222222222222222 69 | @Puerto_6768_7305_1:0:0_0:0:0_11/2 70 | CTGCTGCCTGCAGCCCTGGGATCAAGTACATGTAGTGCGCCACGAGCAAAATGATGGCCACTATTAGGGT 71 | + 72 | 2222222222222222222222222222222222222222222222222222222222222222222222 73 | @Puerto_5435_5937_5:0:0_1:0:0_12/2 74 | CAGAGTCCCCCACTATACACTGTATATTATGGATGAGGCCCACTTCACAGATCCCTCAATTCTAGCAGCA 75 | + 76 | 2222222222222222222222222222222222222222222222222222222222222222222222 77 | @Puerto_9144_9685_4:0:0_0:0:0_13/2 78 | TCAATTGGCTTCACAACGCAATCATCTCCACTGACTGCCATTCGTTTGAGCCTATCCCATCCGTTGCTCT 79 | + 80 | 2222222222222222222222222222222222222222222222222222222222222222222222 81 | -------------------------------------------------------------------------------- /Homework/data/fastq/simulated3.R1.fq: -------------------------------------------------------------------------------- 1 | @Puerto_5207_5777_1:0:0_2:0:0_0/1 2 | TGGGAAAACCAGGAGAGTTCTTCCTGAAATAGTCCGTGAAGCCATAAAAAGAAGACTCCGTACTGTGATC 3 | + 4 | 2222222222222222222222222222222222222222222222222222222222222222222222 5 | @Puerto_4126_4595_1:0:0_0:0:0_1/1 6 | ACTTACCATTTGTCATGGCCCTGGGACTAACCGCTGTGAGGCTGGTCGACCCGATCAACGTGGTGGGACT 7 | + 8 | 2222222222222222222222222222222222222222222222222222222222222222222222 9 | @Puerto_8069_8649_4:0:0_1:0:0_2/1 10 | GCCAGACAACCCCGTTTATTAGAGAGGACGCTGACCCTTGTGTGGGGGCCTCATAGCTTCCATGGTAAGC 11 | + 12 | 2222222222222222222222222222222222222222222222222222222222222222222222 13 | @Puerto_2090_2540_1:0:0_3:0:0_3/1 14 | CTCTAAGCTGATGCTGGAACTTGATCCACCATTTGGGGACTCTTACATTGTCATAGGAGTCGGGGAGAAG 15 | + 16 | 2222222222222222222222222222222222222222222222222222222222222222222222 17 | @Puerto_7758_8266_0:0:0_1:0:0_4/1 18 | GGCATCACCGAGGTGTGCAGAGAAGAGGCCCGCCGCGCCCTCAAGGACGGTGTGGCAACGGGAGGCCATG 19 | + 20 | 2222222222222222222222222222222222222222222222222222222222222222222222 21 | @Puerto_2795_3256_2:0:0_0:0:0_5/1 22 | GAGATTGCCCGTGCCTGTGAACGAGCTGCCCCACGGGTGGAAGGCTTTGGGGAAATCGTATTTCGTCAGA 23 | + 24 | 2222222222222222222222222222222222222222222222222222222222222222222222 25 | @Puerto_2172_2650_0:0:0_2:0:0_6/1 26 | ATACCATCATCCCAGGCTTGCTTGACTGCTGCTGGCAATCTACGGGGGGAGTCAGGATGGTACTTGTACC 27 | + 28 | 2222222222222222222222222222222222222222222222222222222222222222222222 29 | @Puerto_3618_4126_1:0:0_1:0:0_7/1 30 | TTCTTCTTCACACTGCCTTTTCCCTTCAGAGAGAGGAGCAAAAACCCCCCGCAAGTAGCAAGGCCTGCTC 31 | + 32 | 2222222222222222222222222222222222222222222222222222222222222222222222 33 | @Puerto_362_896_1:0:0_1:0:0_8/1 34 | GAAAGATCTGGCTGCCAAGCTGAGAATAATCAATGCTAGGAAGGAGAAGAAGAGACGAGGCGCAGATACT 35 | + 36 | 2222222222222222222222222222222222222222222222222222222222222222222222 37 | @Puerto_8730_9289_0:0:0_1:0:0_9/1 38 | GTTTTCAAGGAAAAAGTGGACACTAGGGTGCCAGACCCCCAAGAAGGCACTCGTCAGGTTATGAGCATGG 39 | + 40 | 2222222222222222222222222222222222222222222222222222222222222222222222 41 | @Puerto_2020_2513_1:0:0_2:0:0_a/1 42 | ACATGCAAACTCTGACCCCAGTTGGGAGGTTGATAACCGCTAACCCCGTACTCACTGAAAGCACTGAGAA 43 | + 44 | 2222222222222222222222222222222222222222222222222222222222222222222222 45 | @Puerto_8179_8741_1:0:0_0:0:0_b/1 46 | GGCTTGAAAAAAGACCAGGAGCCTTTTGTATAAAAGTGTTGTGCCCATACACCAGCACTATGCTGGAAAC 47 | + 48 | 2222222222222222222222222222222222222222222222222222222222222222222222 49 | @Puerto_8541_9051_1:0:0_2:0:0_c/1 50 | TCTTTTCTCTTTTTCCCATCATGTTGTACACACAGCTCTGGCACTCTCCTCTCAGGTGGTGCACTCTTTG 51 | + 52 | 2222222222222222222222222222222222222222222222222222222222222222222222 53 | @Puerto_1817_2345_0:0:0_3:0:0_d/1 54 | CACTGATTTGAAAGGTGCTCCAAAAATTTGATGGATGCGCTTGCCCAATGAGTTGAGAGCGCCTCCAACT 55 | + 56 | 2222222222222222222222222222222222222222222222222222222222222222222222 57 | @Puerto_8936_9483_0:0:0_1:0:0_e/1 58 | CTTTTCCGCTCCCCCTTTGGTCTTGTCTCGAAATAATGTCCATAACTGTTTTCCCTTTTTCAGCTGGTCT 59 | + 60 | 2222222222222222222222222222222222222222222222222222222222222222222222 61 | @Puerto_1548_2094_1:0:0_2:0:0_f/1 62 | TAGAGTTCTCAGTTCTTTCAGTGATTACGGGGTTAGCTGTTATCAACCTCCCAACTGGGGTCAGAGTTTG 63 | + 64 | 2222222222222222222222222222222222222222222222222222222222222222222222 65 | @Puerto_7508_8051_2:0:0_2:0:0_10/1 66 | ACTCTTAATACGGACTATGATCCACCCATAGCTTTGCACCAACACGGGTTCTTCATGACCAGGGCCTCCT 67 | + 68 | 2222222222222222222222222222222222222222222222222222222222222222222222 69 | @Puerto_6768_7305_1:0:0_0:0:0_11/1 70 | CCAGCCAGAATTGCATGTGTCCACATTGTTGTGTTCCTATTGCTGGTGGTGCTCATACCTGAGCCAGAAA 71 | + 72 | 2222222222222222222222222222222222222222222222222222222222222222222222 73 | @Puerto_5435_5937_5:0:0_1:0:0_12/1 74 | GAATGACTCTCTCGCCATCAAGAATGACCGGCTTTAGGCATCTCCTGGAATCTATGACACGGTCAGCTTT 75 | + 76 | 2222222222222222222222222222222222222222222222222222222222222222222222 77 | @Puerto_9144_9685_4:0:0_0:0:0_13/1 78 | TTGAACGAGGATCACTGGATGTGGAGATAGAACACAGGAGGTGGTGTTTAAGGGCTGGGATTACAAAGAC 79 | + 80 | 2222222222222222222222222222222222222222222222222222222222222222222222 81 | -------------------------------------------------------------------------------- /Homework/data/fastq/simulated3.R2.fq: -------------------------------------------------------------------------------- 1 | @Puerto_5207_5777_1:0:0_2:0:0_0/2 2 | TCTGCTGAGCTGTCTGACCCGTTTTCCAGCCTTTGTCCGACAAGCTGCGATCTCATTGCCGTTCCTCACG 3 | + 4 | 2222222222222222222222222222222222222222222222222222222222222222222222 5 | @Puerto_4126_4595_1:0:0_0:0:0_1/2 6 | GTATACGTACCACGCTCCAGCTGCAAAGGGTATGGCTATTGGGTTCATGCCACAGATGGTCATCAGGACC 7 | + 8 | 2222222222222222222222222222222222222222222222222222222222222222222222 9 | @Puerto_8069_8649_4:0:0_1:0:0_2/2 10 | TATGGCGGCTGAGCCGTGTGACAGGTTGCTGTGTGACCTAGGTGAGTCATCAACTAGTCCTGCAGTGGAA 11 | + 12 | 2222222222222222222222222222222222222222222222222222222222222222222222 13 | @Puerto_2090_2540_1:0:0_3:0:0_3/2 14 | TGTACCGCATCTCGACTCCTTCTTTGAGAAGTCCACCGATCACCCCACATCAGCAGAGCCGGCTGTGGAT 15 | + 16 | 2222222222222222222222222222222222222222222222222222222222222222222222 17 | @Puerto_7758_8266_0:0:0_1:0:0_4/2 18 | CGCTGCAGTCGCTCCAGGGTTTCCATGATAGTGCTGGTGTATGGGCACAACACTTTTATACAAAAGGCTC 19 | + 20 | 2222222222222222222222222222222222222222222222222222222222222222222222 21 | @Puerto_2795_3256_2:0:0_0:0:0_5/2 22 | GTATTGTGATGGCTGAGTGGCCCAGCTAAAGACTTGGGTATGATCAGATCACTCTCTTCTATTCCATCTG 23 | + 24 | 2222222222222222222222222222222222222222222222222222222222222222222222 25 | @Puerto_2172_2650_0:0:0_2:0:0_6/2 26 | CACTGGCACAGGAGTGGCAGCACCATTGGAAAAGCATTTGAAGCCACTGTGAGAGGTGCCAAGAGAATGG 27 | + 28 | 2222222222222222222222222222222222222222222222222222222222222222222222 29 | @Puerto_3618_4126_1:0:0_1:0:0_7/2 30 | AAGAAGAGAATGACCACAAAGATCATGATAAGCACATCAATGGCAGTGCTGGTAGCTATGATCCTGGGAG 31 | + 32 | 2222222222222222222222222222222222222222222222222222222222222222222222 33 | @Puerto_362_896_1:0:0_1:0:0_8/2 34 | GGCAGCTGCTGCTAACGCGAAGCCAGGGTTCCTGAATATCCAATTTTCGACTCTAATCAAGTGGTTTGTG 35 | + 36 | 2222222222222222222222222222222222222222222222222222222222222222222222 37 | @Puerto_8730_9289_0:0:0_1:0:0_9/2 38 | GTGTCCCAGCCAGCAGTGTCATCTGCATACATCCTTCCTCCTGGTATACGACTCATCTGTTCTAGGACAT 39 | + 40 | 2222222222222222222222222222222222222222222222222222222222222222222222 41 | @Puerto_2020_2513_1:0:0_2:0:0_a/2 42 | GACGTGCACCGAGCACCCCACATCAGCAGAGACGGCTGTGGATAAGAAGATCAACACTCCCCCTAAGGCC 43 | + 44 | 2222222222222222222222222222222222222222222222222222222222222222222222 45 | @Puerto_8179_8741_1:0:0_0:0:0_b/2 46 | TTCCTTGAAAACTCTTTGCTGACCATACGGTGTGGTGTCGGTCATGGCTATTCCTGTGACTCCAGTCACC 47 | + 48 | 2222222222222222222222222222222222222222222222222222222222222222222222 49 | @Puerto_8541_9051_1:0:0_2:0:0_c/2 50 | ACGTGGTTCTTTGACGAGAACCACCCATATAGGACATGGGCTTACCATGGAAGCTATGAGGCCCCCAGAC 51 | + 52 | 2222222222222222222222222222222222222222222222222222222222222222222222 53 | @Puerto_1817_2345_0:0:0_3:0:0_d/2 54 | AAAGGGAAGGCTGTCCTCTGGCCACTTGAAATGTCGCCTGAAAATGGATAAACTTAGATTGAAGGGCGTG 55 | + 56 | 2222222222222222222222222222222222222222222222222222222222222222222222 57 | @Puerto_8936_9483_0:0:0_1:0:0_e/2 58 | AGTGGAAGCTGTGAACGATCCAAGGTTCTGGGCTCTAGTGGACAAGGAAAGAGAGCACCACCTGAGAGGA 59 | + 60 | 2222222222222222222222222222222222222222222222222222222222222222222222 61 | @Puerto_1548_2094_1:0:0_2:0:0_f/2 62 | GAACGGAGGACAGGCCTTGACTTTTCAGATTTGTATTACTTGACTATGAATAACAAGCACTGGTTGGTTC 63 | + 64 | 2222222222222222222222222222222222222222222222222222222222222222222222 65 | @Puerto_7508_8051_2:0:0_2:0:0_10/2 66 | GATCACAGCCGCAACTTCCACTTTTTGGGCAGGCTCTCCGAACAAGTACTGGAACTCCTCTACAGCCACT 67 | + 68 | 2222222222222222222222222222222222222222222222222222222222222222222222 69 | @Puerto_6768_7305_1:0:0_0:0:0_11/2 70 | CTGCTGCCTGCAGCCCTGGGATCAAGTACATGTAGTGCGCCACGAGCAAAATGATGGCCACTATTAGGGT 71 | + 72 | 2222222222222222222222222222222222222222222222222222222222222222222222 73 | @Puerto_5435_5937_5:0:0_1:0:0_12/2 74 | CAGAGTCCCCCACTATACACTGTATATTATGGATGAGGCCCACTTCACAGATCCCTCAATTCTAGCAGCA 75 | + 76 | 2222222222222222222222222222222222222222222222222222222222222222222222 77 | @Puerto_9144_9685_4:0:0_0:0:0_13/2 78 | TCAATTGGCTTCACAACGCAATCATCTCCACTGACTGCCATTCGTTTGAGCCTATCCCATCCGTTGCTCT 79 | + 80 | 2222222222222222222222222222222222222222222222222222222222222222222222 81 | -------------------------------------------------------------------------------- /Homework/data/fastq/simulated4.R1.fq: -------------------------------------------------------------------------------- 1 | @Puerto_5207_5777_1:0:0_2:0:0_0/1 2 | TGGGAAAACCAGGAGAGTTCTTCCTGAAATAGTCCGTGAAGCCATAAAAAGAAGACTCCGTACTGTGATC 3 | + 4 | 2222222222222222222222222222222222222222222222222222222222222222222222 5 | @Puerto_4126_4595_1:0:0_0:0:0_1/1 6 | ACTTACCATTTGTCATGGCCCTGGGACTAACCGCTGTGAGGCTGGTCGACCCGATCAACGTGGTGGGACT 7 | + 8 | 2222222222222222222222222222222222222222222222222222222222222222222222 9 | @Puerto_8069_8649_4:0:0_1:0:0_2/1 10 | GCCAGACAACCCCGTTTATTAGAGAGGACGCTGACCCTTGTGTGGGGGCCTCATAGCTTCCATGGTAAGC 11 | + 12 | 2222222222222222222222222222222222222222222222222222222222222222222222 13 | @Puerto_2090_2540_1:0:0_3:0:0_3/1 14 | CTCTAAGCTGATGCTGGAACTTGATCCACCATTTGGGGACTCTTACATTGTCATAGGAGTCGGGGAGAAG 15 | + 16 | 2222222222222222222222222222222222222222222222222222222222222222222222 17 | @Puerto_7758_8266_0:0:0_1:0:0_4/1 18 | GGCATCACCGAGGTGTGCAGAGAAGAGGCCCGCCGCGCCCTCAAGGACGGTGTGGCAACGGGAGGCCATG 19 | + 20 | 2222222222222222222222222222222222222222222222222222222222222222222222 21 | @Puerto_2795_3256_2:0:0_0:0:0_5/1 22 | GAGATTGCCCGTGCCTGTGAACGAGCTGCCCCACGGGTGGAAGGCTTTGGGGAAATCGTATTTCGTCAGA 23 | + 24 | 2222222222222222222222222222222222222222222222222222222222222222222222 25 | @Puerto_2172_2650_0:0:0_2:0:0_6/1 26 | ATACCATCATCCCAGGCTTGCTTGACTGCTGCTGGCAATCTACGGGGGGAGTCAGGATGGTACTTGTACC 27 | + 28 | 2222222222222222222222222222222222222222222222222222222222222222222222 29 | @Puerto_3618_4126_1:0:0_1:0:0_7/1 30 | TTCTTCTTCACACTGCCTTTTCCCTTCAGAGAGAGGAGCAAAAACCCCCCGCAAGTAGCAAGGCCTGCTC 31 | + 32 | 2222222222222222222222222222222222222222222222222222222222222222222222 33 | @Puerto_362_896_1:0:0_1:0:0_8/1 34 | GAAAGATCTGGCTGCCAAGCTGAGAATAATCAATGCTAGGAAGGAGAAGAAGAGACGAGGCGCAGATACT 35 | + 36 | 2222222222222222222222222222222222222222222222222222222222222222222222 37 | @Puerto_8730_9289_0:0:0_1:0:0_9/1 38 | GTTTTCAAGGAAAAAGTGGACACTAGGGTGCCAGACCCCCAAGAAGGCACTCGTCAGGTTATGAGCATGG 39 | + 40 | 2222222222222222222222222222222222222222222222222222222222222222222222 41 | @Puerto_2020_2513_1:0:0_2:0:0_a/1 42 | ACATGCAAACTCTGACCCCAGTTGGGAGGTTGATAACCGCTAACCCCGTACTCACTGAAAGCACTGAGAA 43 | + 44 | 2222222222222222222222222222222222222222222222222222222222222222222222 45 | @Puerto_8179_8741_1:0:0_0:0:0_b/1 46 | GGCTTGAAAAAAGACCAGGAGCCTTTTGTATAAAAGTGTTGTGCCCATACACCAGCACTATGCTGGAAAC 47 | + 48 | 2222222222222222222222222222222222222222222222222222222222222222222222 49 | @Puerto_8541_9051_1:0:0_2:0:0_c/1 50 | TCTTTTCTCTTTTTCCCATCATGTTGTACACACAGCTCTGGCACTCTCCTCTCAGGTGGTGCACTCTTTG 51 | + 52 | 2222222222222222222222222222222222222222222222222222222222222222222222 53 | @Puerto_1817_2345_0:0:0_3:0:0_d/1 54 | CACTGATTTGAAAGGTGCTCCAAAAATTTGATGGATGCGCTTGCCCAATGAGTTGAGAGCGCCTCCAACT 55 | + 56 | 2222222222222222222222222222222222222222222222222222222222222222222222 57 | @Puerto_8936_9483_0:0:0_1:0:0_e/1 58 | CTTTTCCGCTCCCCCTTTGGTCTTGTCTCGAAATAATGTCCATAACTGTTTTCCCTTTTTCAGCTGGTCT 59 | + 60 | 2222222222222222222222222222222222222222222222222222222222222222222222 61 | @Puerto_1548_2094_1:0:0_2:0:0_f/1 62 | TAGAGTTCTCAGTTCTTTCAGTGATTACGGGGTTAGCTGTTATCAACCTCCCAACTGGGGTCAGAGTTTG 63 | + 64 | 2222222222222222222222222222222222222222222222222222222222222222222222 65 | @Puerto_7508_8051_2:0:0_2:0:0_10/1 66 | ACTCTTAATACGGACTATGATCCACCCATAGCTTTGCACCAACACGGGTTCTTCATGACCAGGGCCTCCT 67 | + 68 | 2222222222222222222222222222222222222222222222222222222222222222222222 69 | @Puerto_6768_7305_1:0:0_0:0:0_11/1 70 | CCAGCCAGAATTGCATGTGTCCACATTGTTGTGTTCCTATTGCTGGTGGTGCTCATACCTGAGCCAGAAA 71 | + 72 | 2222222222222222222222222222222222222222222222222222222222222222222222 73 | @Puerto_5435_5937_5:0:0_1:0:0_12/1 74 | GAATGACTCTCTCGCCATCAAGAATGACCGGCTTTAGGCATCTCCTGGAATCTATGACACGGTCAGCTTT 75 | + 76 | 2222222222222222222222222222222222222222222222222222222222222222222222 77 | @Puerto_9144_9685_4:0:0_0:0:0_13/1 78 | TTGAACGAGGATCACTGGATGTGGAGATAGAACACAGGAGGTGGTGTTTAAGGGCTGGGATTACAAAGAC 79 | + 80 | 2222222222222222222222222222222222222222222222222222222222222222222222 81 | -------------------------------------------------------------------------------- /Homework/data/fastq/simulated4.R2.fq: -------------------------------------------------------------------------------- 1 | @Puerto_5207_5777_1:0:0_2:0:0_0/2 2 | TCTGCTGAGCTGTCTGACCCGTTTTCCAGCCTTTGTCCGACAAGCTGCGATCTCATTGCCGTTCCTCACG 3 | + 4 | 2222222222222222222222222222222222222222222222222222222222222222222222 5 | @Puerto_4126_4595_1:0:0_0:0:0_1/2 6 | GTATACGTACCACGCTCCAGCTGCAAAGGGTATGGCTATTGGGTTCATGCCACAGATGGTCATCAGGACC 7 | + 8 | 2222222222222222222222222222222222222222222222222222222222222222222222 9 | @Puerto_8069_8649_4:0:0_1:0:0_2/2 10 | TATGGCGGCTGAGCCGTGTGACAGGTTGCTGTGTGACCTAGGTGAGTCATCAACTAGTCCTGCAGTGGAA 11 | + 12 | 2222222222222222222222222222222222222222222222222222222222222222222222 13 | @Puerto_2090_2540_1:0:0_3:0:0_3/2 14 | TGTACCGCATCTCGACTCCTTCTTTGAGAAGTCCACCGATCACCCCACATCAGCAGAGCCGGCTGTGGAT 15 | + 16 | 2222222222222222222222222222222222222222222222222222222222222222222222 17 | @Puerto_7758_8266_0:0:0_1:0:0_4/2 18 | CGCTGCAGTCGCTCCAGGGTTTCCATGATAGTGCTGGTGTATGGGCACAACACTTTTATACAAAAGGCTC 19 | + 20 | 2222222222222222222222222222222222222222222222222222222222222222222222 21 | @Puerto_2795_3256_2:0:0_0:0:0_5/2 22 | GTATTGTGATGGCTGAGTGGCCCAGCTAAAGACTTGGGTATGATCAGATCACTCTCTTCTATTCCATCTG 23 | + 24 | 2222222222222222222222222222222222222222222222222222222222222222222222 25 | @Puerto_2172_2650_0:0:0_2:0:0_6/2 26 | CACTGGCACAGGAGTGGCAGCACCATTGGAAAAGCATTTGAAGCCACTGTGAGAGGTGCCAAGAGAATGG 27 | + 28 | 2222222222222222222222222222222222222222222222222222222222222222222222 29 | @Puerto_3618_4126_1:0:0_1:0:0_7/2 30 | AAGAAGAGAATGACCACAAAGATCATGATAAGCACATCAATGGCAGTGCTGGTAGCTATGATCCTGGGAG 31 | + 32 | 2222222222222222222222222222222222222222222222222222222222222222222222 33 | @Puerto_362_896_1:0:0_1:0:0_8/2 34 | GGCAGCTGCTGCTAACGCGAAGCCAGGGTTCCTGAATATCCAATTTTCGACTCTAATCAAGTGGTTTGTG 35 | + 36 | 2222222222222222222222222222222222222222222222222222222222222222222222 37 | @Puerto_8730_9289_0:0:0_1:0:0_9/2 38 | GTGTCCCAGCCAGCAGTGTCATCTGCATACATCCTTCCTCCTGGTATACGACTCATCTGTTCTAGGACAT 39 | + 40 | 2222222222222222222222222222222222222222222222222222222222222222222222 41 | @Puerto_2020_2513_1:0:0_2:0:0_a/2 42 | GACGTGCACCGAGCACCCCACATCAGCAGAGACGGCTGTGGATAAGAAGATCAACACTCCCCCTAAGGCC 43 | + 44 | 2222222222222222222222222222222222222222222222222222222222222222222222 45 | @Puerto_8179_8741_1:0:0_0:0:0_b/2 46 | TTCCTTGAAAACTCTTTGCTGACCATACGGTGTGGTGTCGGTCATGGCTATTCCTGTGACTCCAGTCACC 47 | + 48 | 2222222222222222222222222222222222222222222222222222222222222222222222 49 | @Puerto_8541_9051_1:0:0_2:0:0_c/2 50 | ACGTGGTTCTTTGACGAGAACCACCCATATAGGACATGGGCTTACCATGGAAGCTATGAGGCCCCCAGAC 51 | + 52 | 2222222222222222222222222222222222222222222222222222222222222222222222 53 | @Puerto_1817_2345_0:0:0_3:0:0_d/2 54 | AAAGGGAAGGCTGTCCTCTGGCCACTTGAAATGTCGCCTGAAAATGGATAAACTTAGATTGAAGGGCGTG 55 | + 56 | 2222222222222222222222222222222222222222222222222222222222222222222222 57 | @Puerto_8936_9483_0:0:0_1:0:0_e/2 58 | AGTGGAAGCTGTGAACGATCCAAGGTTCTGGGCTCTAGTGGACAAGGAAAGAGAGCACCACCTGAGAGGA 59 | + 60 | 2222222222222222222222222222222222222222222222222222222222222222222222 61 | @Puerto_1548_2094_1:0:0_2:0:0_f/2 62 | GAACGGAGGACAGGCCTTGACTTTTCAGATTTGTATTACTTGACTATGAATAACAAGCACTGGTTGGTTC 63 | + 64 | 2222222222222222222222222222222222222222222222222222222222222222222222 65 | @Puerto_7508_8051_2:0:0_2:0:0_10/2 66 | GATCACAGCCGCAACTTCCACTTTTTGGGCAGGCTCTCCGAACAAGTACTGGAACTCCTCTACAGCCACT 67 | + 68 | 2222222222222222222222222222222222222222222222222222222222222222222222 69 | @Puerto_6768_7305_1:0:0_0:0:0_11/2 70 | CTGCTGCCTGCAGCCCTGGGATCAAGTACATGTAGTGCGCCACGAGCAAAATGATGGCCACTATTAGGGT 71 | + 72 | 2222222222222222222222222222222222222222222222222222222222222222222222 73 | @Puerto_5435_5937_5:0:0_1:0:0_12/2 74 | CAGAGTCCCCCACTATACACTGTATATTATGGATGAGGCCCACTTCACAGATCCCTCAATTCTAGCAGCA 75 | + 76 | 2222222222222222222222222222222222222222222222222222222222222222222222 77 | @Puerto_9144_9685_4:0:0_0:0:0_13/2 78 | TCAATTGGCTTCACAACGCAATCATCTCCACTGACTGCCATTCGTTTGAGCCTATCCCATCCGTTGCTCT 79 | + 80 | 2222222222222222222222222222222222222222222222222222222222222222222222 81 | -------------------------------------------------------------------------------- /Homework/data/fastq/simulated5.R1.fq: -------------------------------------------------------------------------------- 1 | @Puerto_5207_5777_1:0:0_2:0:0_0/1 2 | TGGGAAAACCAGGAGAGTTCTTCCTGAAATAGTCCGTGAAGCCATAAAAAGAAGACTCCGTACTGTGATC 3 | + 4 | 2222222222222222222222222222222222222222222222222222222222222222222222 5 | @Puerto_4126_4595_1:0:0_0:0:0_1/1 6 | ACTTACCATTTGTCATGGCCCTGGGACTAACCGCTGTGAGGCTGGTCGACCCGATCAACGTGGTGGGACT 7 | + 8 | 2222222222222222222222222222222222222222222222222222222222222222222222 9 | @Puerto_8069_8649_4:0:0_1:0:0_2/1 10 | GCCAGACAACCCCGTTTATTAGAGAGGACGCTGACCCTTGTGTGGGGGCCTCATAGCTTCCATGGTAAGC 11 | + 12 | 2222222222222222222222222222222222222222222222222222222222222222222222 13 | @Puerto_2090_2540_1:0:0_3:0:0_3/1 14 | CTCTAAGCTGATGCTGGAACTTGATCCACCATTTGGGGACTCTTACATTGTCATAGGAGTCGGGGAGAAG 15 | + 16 | 2222222222222222222222222222222222222222222222222222222222222222222222 17 | @Puerto_7758_8266_0:0:0_1:0:0_4/1 18 | GGCATCACCGAGGTGTGCAGAGAAGAGGCCCGCCGCGCCCTCAAGGACGGTGTGGCAACGGGAGGCCATG 19 | + 20 | 2222222222222222222222222222222222222222222222222222222222222222222222 21 | @Puerto_2795_3256_2:0:0_0:0:0_5/1 22 | GAGATTGCCCGTGCCTGTGAACGAGCTGCCCCACGGGTGGAAGGCTTTGGGGAAATCGTATTTCGTCAGA 23 | + 24 | 2222222222222222222222222222222222222222222222222222222222222222222222 25 | @Puerto_2172_2650_0:0:0_2:0:0_6/1 26 | ATACCATCATCCCAGGCTTGCTTGACTGCTGCTGGCAATCTACGGGGGGAGTCAGGATGGTACTTGTACC 27 | + 28 | 2222222222222222222222222222222222222222222222222222222222222222222222 29 | @Puerto_3618_4126_1:0:0_1:0:0_7/1 30 | TTCTTCTTCACACTGCCTTTTCCCTTCAGAGAGAGGAGCAAAAACCCCCCGCAAGTAGCAAGGCCTGCTC 31 | + 32 | 2222222222222222222222222222222222222222222222222222222222222222222222 33 | @Puerto_362_896_1:0:0_1:0:0_8/1 34 | GAAAGATCTGGCTGCCAAGCTGAGAATAATCAATGCTAGGAAGGAGAAGAAGAGACGAGGCGCAGATACT 35 | + 36 | 2222222222222222222222222222222222222222222222222222222222222222222222 37 | @Puerto_8730_9289_0:0:0_1:0:0_9/1 38 | GTTTTCAAGGAAAAAGTGGACACTAGGGTGCCAGACCCCCAAGAAGGCACTCGTCAGGTTATGAGCATGG 39 | + 40 | 2222222222222222222222222222222222222222222222222222222222222222222222 41 | @Puerto_2020_2513_1:0:0_2:0:0_a/1 42 | ACATGCAAACTCTGACCCCAGTTGGGAGGTTGATAACCGCTAACCCCGTACTCACTGAAAGCACTGAGAA 43 | + 44 | 2222222222222222222222222222222222222222222222222222222222222222222222 45 | @Puerto_8179_8741_1:0:0_0:0:0_b/1 46 | GGCTTGAAAAAAGACCAGGAGCCTTTTGTATAAAAGTGTTGTGCCCATACACCAGCACTATGCTGGAAAC 47 | + 48 | 2222222222222222222222222222222222222222222222222222222222222222222222 49 | @Puerto_8541_9051_1:0:0_2:0:0_c/1 50 | TCTTTTCTCTTTTTCCCATCATGTTGTACACACAGCTCTGGCACTCTCCTCTCAGGTGGTGCACTCTTTG 51 | + 52 | 2222222222222222222222222222222222222222222222222222222222222222222222 53 | @Puerto_1817_2345_0:0:0_3:0:0_d/1 54 | CACTGATTTGAAAGGTGCTCCAAAAATTTGATGGATGCGCTTGCCCAATGAGTTGAGAGCGCCTCCAACT 55 | + 56 | 2222222222222222222222222222222222222222222222222222222222222222222222 57 | @Puerto_8936_9483_0:0:0_1:0:0_e/1 58 | CTTTTCCGCTCCCCCTTTGGTCTTGTCTCGAAATAATGTCCATAACTGTTTTCCCTTTTTCAGCTGGTCT 59 | + 60 | 2222222222222222222222222222222222222222222222222222222222222222222222 61 | @Puerto_1548_2094_1:0:0_2:0:0_f/1 62 | TAGAGTTCTCAGTTCTTTCAGTGATTACGGGGTTAGCTGTTATCAACCTCCCAACTGGGGTCAGAGTTTG 63 | + 64 | 2222222222222222222222222222222222222222222222222222222222222222222222 65 | @Puerto_7508_8051_2:0:0_2:0:0_10/1 66 | ACTCTTAATACGGACTATGATCCACCCATAGCTTTGCACCAACACGGGTTCTTCATGACCAGGGCCTCCT 67 | + 68 | 2222222222222222222222222222222222222222222222222222222222222222222222 69 | @Puerto_6768_7305_1:0:0_0:0:0_11/1 70 | CCAGCCAGAATTGCATGTGTCCACATTGTTGTGTTCCTATTGCTGGTGGTGCTCATACCTGAGCCAGAAA 71 | + 72 | 2222222222222222222222222222222222222222222222222222222222222222222222 73 | @Puerto_5435_5937_5:0:0_1:0:0_12/1 74 | GAATGACTCTCTCGCCATCAAGAATGACCGGCTTTAGGCATCTCCTGGAATCTATGACACGGTCAGCTTT 75 | + 76 | 2222222222222222222222222222222222222222222222222222222222222222222222 77 | @Puerto_9144_9685_4:0:0_0:0:0_13/1 78 | TTGAACGAGGATCACTGGATGTGGAGATAGAACACAGGAGGTGGTGTTTAAGGGCTGGGATTACAAAGAC 79 | + 80 | 2222222222222222222222222222222222222222222222222222222222222222222222 81 | -------------------------------------------------------------------------------- /Homework/data/fastq/simulated5.R2.fq: -------------------------------------------------------------------------------- 1 | @Puerto_5207_5777_1:0:0_2:0:0_0/2 2 | TCTGCTGAGCTGTCTGACCCGTTTTCCAGCCTTTGTCCGACAAGCTGCGATCTCATTGCCGTTCCTCACG 3 | + 4 | 2222222222222222222222222222222222222222222222222222222222222222222222 5 | @Puerto_4126_4595_1:0:0_0:0:0_1/2 6 | GTATACGTACCACGCTCCAGCTGCAAAGGGTATGGCTATTGGGTTCATGCCACAGATGGTCATCAGGACC 7 | + 8 | 2222222222222222222222222222222222222222222222222222222222222222222222 9 | @Puerto_8069_8649_4:0:0_1:0:0_2/2 10 | TATGGCGGCTGAGCCGTGTGACAGGTTGCTGTGTGACCTAGGTGAGTCATCAACTAGTCCTGCAGTGGAA 11 | + 12 | 2222222222222222222222222222222222222222222222222222222222222222222222 13 | @Puerto_2090_2540_1:0:0_3:0:0_3/2 14 | TGTACCGCATCTCGACTCCTTCTTTGAGAAGTCCACCGATCACCCCACATCAGCAGAGCCGGCTGTGGAT 15 | + 16 | 2222222222222222222222222222222222222222222222222222222222222222222222 17 | @Puerto_7758_8266_0:0:0_1:0:0_4/2 18 | CGCTGCAGTCGCTCCAGGGTTTCCATGATAGTGCTGGTGTATGGGCACAACACTTTTATACAAAAGGCTC 19 | + 20 | 2222222222222222222222222222222222222222222222222222222222222222222222 21 | @Puerto_2795_3256_2:0:0_0:0:0_5/2 22 | GTATTGTGATGGCTGAGTGGCCCAGCTAAAGACTTGGGTATGATCAGATCACTCTCTTCTATTCCATCTG 23 | + 24 | 2222222222222222222222222222222222222222222222222222222222222222222222 25 | @Puerto_2172_2650_0:0:0_2:0:0_6/2 26 | CACTGGCACAGGAGTGGCAGCACCATTGGAAAAGCATTTGAAGCCACTGTGAGAGGTGCCAAGAGAATGG 27 | + 28 | 2222222222222222222222222222222222222222222222222222222222222222222222 29 | @Puerto_3618_4126_1:0:0_1:0:0_7/2 30 | AAGAAGAGAATGACCACAAAGATCATGATAAGCACATCAATGGCAGTGCTGGTAGCTATGATCCTGGGAG 31 | + 32 | 2222222222222222222222222222222222222222222222222222222222222222222222 33 | @Puerto_362_896_1:0:0_1:0:0_8/2 34 | GGCAGCTGCTGCTAACGCGAAGCCAGGGTTCCTGAATATCCAATTTTCGACTCTAATCAAGTGGTTTGTG 35 | + 36 | 2222222222222222222222222222222222222222222222222222222222222222222222 37 | @Puerto_8730_9289_0:0:0_1:0:0_9/2 38 | GTGTCCCAGCCAGCAGTGTCATCTGCATACATCCTTCCTCCTGGTATACGACTCATCTGTTCTAGGACAT 39 | + 40 | 2222222222222222222222222222222222222222222222222222222222222222222222 41 | @Puerto_2020_2513_1:0:0_2:0:0_a/2 42 | GACGTGCACCGAGCACCCCACATCAGCAGAGACGGCTGTGGATAAGAAGATCAACACTCCCCCTAAGGCC 43 | + 44 | 2222222222222222222222222222222222222222222222222222222222222222222222 45 | @Puerto_8179_8741_1:0:0_0:0:0_b/2 46 | TTCCTTGAAAACTCTTTGCTGACCATACGGTGTGGTGTCGGTCATGGCTATTCCTGTGACTCCAGTCACC 47 | + 48 | 2222222222222222222222222222222222222222222222222222222222222222222222 49 | @Puerto_8541_9051_1:0:0_2:0:0_c/2 50 | ACGTGGTTCTTTGACGAGAACCACCCATATAGGACATGGGCTTACCATGGAAGCTATGAGGCCCCCAGAC 51 | + 52 | 2222222222222222222222222222222222222222222222222222222222222222222222 53 | @Puerto_1817_2345_0:0:0_3:0:0_d/2 54 | AAAGGGAAGGCTGTCCTCTGGCCACTTGAAATGTCGCCTGAAAATGGATAAACTTAGATTGAAGGGCGTG 55 | + 56 | 2222222222222222222222222222222222222222222222222222222222222222222222 57 | @Puerto_8936_9483_0:0:0_1:0:0_e/2 58 | AGTGGAAGCTGTGAACGATCCAAGGTTCTGGGCTCTAGTGGACAAGGAAAGAGAGCACCACCTGAGAGGA 59 | + 60 | 2222222222222222222222222222222222222222222222222222222222222222222222 61 | @Puerto_1548_2094_1:0:0_2:0:0_f/2 62 | GAACGGAGGACAGGCCTTGACTTTTCAGATTTGTATTACTTGACTATGAATAACAAGCACTGGTTGGTTC 63 | + 64 | 2222222222222222222222222222222222222222222222222222222222222222222222 65 | @Puerto_7508_8051_2:0:0_2:0:0_10/2 66 | GATCACAGCCGCAACTTCCACTTTTTGGGCAGGCTCTCCGAACAAGTACTGGAACTCCTCTACAGCCACT 67 | + 68 | 2222222222222222222222222222222222222222222222222222222222222222222222 69 | @Puerto_6768_7305_1:0:0_0:0:0_11/2 70 | CTGCTGCCTGCAGCCCTGGGATCAAGTACATGTAGTGCGCCACGAGCAAAATGATGGCCACTATTAGGGT 71 | + 72 | 2222222222222222222222222222222222222222222222222222222222222222222222 73 | @Puerto_5435_5937_5:0:0_1:0:0_12/2 74 | CAGAGTCCCCCACTATACACTGTATATTATGGATGAGGCCCACTTCACAGATCCCTCAATTCTAGCAGCA 75 | + 76 | 2222222222222222222222222222222222222222222222222222222222222222222222 77 | @Puerto_9144_9685_4:0:0_0:0:0_13/2 78 | TCAATTGGCTTCACAACGCAATCATCTCCACTGACTGCCATTCGTTTGAGCCTATCCCATCCGTTGCTCT 79 | + 80 | 2222222222222222222222222222222222222222222222222222222222222222222222 81 | -------------------------------------------------------------------------------- /Homework/data/tmp/file1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuLab/Applied-Bioinformatics/7c01300871e64c09fec7ade1af4c2f3c8bb074e5/Homework/data/tmp/file1.txt -------------------------------------------------------------------------------- /Homework/data/tmp/file10.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuLab/Applied-Bioinformatics/7c01300871e64c09fec7ade1af4c2f3c8bb074e5/Homework/data/tmp/file10.txt 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\n", 8 | "Try out different tools you haven't yet, if you feel creative (or to challenge yoursef)" 9 | ] 10 | }, 11 | { 12 | "cell_type": "markdown", 13 | "metadata": {}, 14 | "source": [ 15 | "## Now\n", 16 | "Filtering and normalizing your data for DESeq2
\n", 17 | "https://github.com/SuLab/Applied-Bioinformatics/blob/Fall-2018/Unit2-RNAseq/3.6_DESeq2_differential_expression_analysis.ipynb \n", 18 | "\n", 19 | "\n", 20 | "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97919
\n", 21 | "Look familiar?\n", 22 | "\n", 23 | "1. Get the files into your data folder\n", 24 | "2. Convert these to a 'matrix'for DESeq2. Compare how these look in contrast to the output count matrix you created. What's different and why?\n", 25 | "3. Convert from character to numeric\n", 26 | "4. Normalize matrix, what does this mean?? (DESeq fxn) " 27 | ] 28 | }, 29 | { 30 | "cell_type": "code", 31 | "execution_count": null, 32 | "metadata": {}, 33 | "outputs": [], 34 | "source": [ 35 | "# Good habits: Always check directory\n", 36 | "getwd()" 37 | ] 38 | }, 39 | { 40 | "cell_type": "code", 41 | "execution_count": null, 42 | "metadata": {}, 43 | "outputs": [], 44 | "source": [ 45 | "# Assign your files to a... how can we figure out what 'counts_files' is?\n", 46 | "dir_counts <- \"/home_local/instructor-abcb2020/abcb2020/source/HW8/data/Demos/htseq_out\" # note method used\n", 47 | "counts_files <- list.files(dir_counts)\n", 48 | "counts_files" 49 | ] 50 | }, 51 | { 52 | "cell_type": "code", 53 | "execution_count": null, 54 | "metadata": {}, 55 | "outputs": [], 56 | "source": [ 57 | "# Install/load DESeq2 package (now we're coming full-circle up from where we started week 5)\n", 58 | "\n", 59 | "library(\"DESeq2\")\n", 60 | "packageVersion(\"DESeq2\")" 61 | ] 62 | }, 63 | { 64 | "cell_type": "code", 65 | "execution_count": null, 66 | "metadata": {}, 67 | "outputs": [], 68 | "source": [ 69 | "# run...?\n", 70 | "dds1 <- DESeqDataSetFromHTSeqCount(sampleTable = ?, \n", 71 | " directory = dir_counts, \n", 72 | " design = ~ group)" 73 | ] 74 | }, 75 | { 76 | "cell_type": "code", 77 | "execution_count": null, 78 | "metadata": {}, 79 | "outputs": [], 80 | "source": [ 81 | "# Create a 'metadata' sheet (you always need this!)\n", 82 | "samplesInfo <- as.data.frame(matrix(ncol=2, nrow=length(counts_files))) \n", 83 | "samplesInfo$samplename <- counts_files \n", 84 | "samplesInfo$filename <- counts_files \n", 85 | "samplesInfo$group <- c(\"mock\", \"ZIKV\", \"mock\", \"ZIKV\", \"mock\", \"ZIKV\") \n", 86 | "\n", 87 | "samplesInfo # What do we need to change?" 88 | ] 89 | }, 90 | { 91 | "cell_type": "code", 92 | "execution_count": null, 93 | "metadata": {}, 94 | "outputs": [], 95 | "source": [ 96 | "#Remove the blank columns (RE setting up your notebook cells to then script)\n", 97 | "\n", 98 | "samplesInfo <- samplesInfo[,-c(1:2)]\n", 99 | "samplesInfo" 100 | ] 101 | }, 102 | { 103 | "cell_type": "code", 104 | "execution_count": null, 105 | "metadata": {}, 106 | "outputs": [], 107 | "source": [ 108 | "# Prep for DESeq2 (what are each of these steps?)\n", 109 | "\n", 110 | "# What does this format remind you of from week 5?\n", 111 | "dds1 <- DESeqDataSetFromHTSeqCount(sampleTable = samplesInfo, \n", 112 | " directory = dir_counts, \n", 113 | " design = ~ group)" 114 | ] 115 | }, 116 | { 117 | "cell_type": "code", 118 | "execution_count": null, 119 | "metadata": {}, 120 | "outputs": [], 121 | "source": [ 122 | "# How to fix? Convert to numeric design = ~ group)" 123 | ] 124 | }, 125 | { 126 | "cell_type": "code", 127 | "execution_count": null, 128 | "metadata": {}, 129 | "outputs": [], 130 | "source": [ 131 | "# Explore the data\n", 132 | "colData(dds1)" 133 | ] 134 | }, 135 | { 136 | "cell_type": "markdown", 137 | "metadata": {}, 138 | "source": [ 139 | "Notes on normalization and filtering matrix here
\n", 140 | "ie https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#data-transformations-and-visualization
\n", 141 | "\n", 142 | "Feel welcome to add others" 143 | ] 144 | }, 145 | { 146 | "cell_type": "markdown", 147 | "metadata": {}, 148 | "source": [ 149 | "### B8.bb DESeq2" 150 | ] 151 | }, 152 | { 153 | "cell_type": "markdown", 154 | "metadata": {}, 155 | "source": [ 156 | "DESeq2 fxn\n", 157 | "https://lashlock.github.io/compbio/R_presentation.html" 158 | ] 159 | }, 160 | { 161 | "cell_type": "markdown", 162 | "metadata": {}, 163 | "source": [ 164 | "What can you do to check variations of normalizing your data?" 165 | ] 166 | }, 167 | { 168 | "cell_type": "markdown", 169 | "metadata": {}, 170 | "source": [ 171 | "What is a scientific question we could ask on this data that can be related to a volcano plot or PCA plot?" 172 | ] 173 | } 174 | ], 175 | "metadata": { 176 | "kernelspec": { 177 | "display_name": "R", 178 | "language": "R", 179 | "name": "ir" 180 | }, 181 | "language_info": { 182 | "codemirror_mode": "r", 183 | "file_extension": ".r", 184 | "mimetype": "text/x-r-source", 185 | "name": "R", 186 | "pygments_lexer": "r", 187 | "version": "3.5.1" 188 | } 189 | }, 190 | "nbformat": 4, 191 | "nbformat_minor": 4 192 | } 193 | -------------------------------------------------------------------------------- /Lectures/B8.a_R-Expression-Analysis.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuLab/Applied-Bioinformatics/7c01300871e64c09fec7ade1af4c2f3c8bb074e5/Lectures/B8.a_R-Expression-Analysis.pptx -------------------------------------------------------------------------------- /Lectures/B8.b_R-DESeq2Enrichment.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuLab/Applied-Bioinformatics/7c01300871e64c09fec7ade1af4c2f3c8bb074e5/Lectures/B8.b_R-DESeq2Enrichment.pptx -------------------------------------------------------------------------------- /Lectures/B9.a-Data_and_Demo/datasets/Wang_Dapeng_IMMUNITY_2018_simp_colnames.csv: -------------------------------------------------------------------------------- 1 | sample_names,day,cell_type,replicate 2 | Day5_EEC_1,Day5,EEC,1 3 | Day5_SLEC_1,Day5,SLEC,1 4 | Day5_EEC_2,Day5,EEC,2 5 | Day5_SLEC_2,Day5,SLEC,2 6 | Day8_EEC_1,Day8,EEC,1 7 | Day8_SLEC_1,Day8,SLEC,1 8 | Day8_MPEC_1,Day8,MPEC,1 9 | Day8_EEC_2,Day8,EEC,2 10 | Day8_SLEC_2,Day8,SLEC,2 11 | Day8_MPEC_2,Day8,MPEC,2 12 | -------------------------------------------------------------------------------- /Lectures/B9.a_R-RNASeq-PCA.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuLab/Applied-Bioinformatics/7c01300871e64c09fec7ade1af4c2f3c8bb074e5/Lectures/B9.a_R-RNASeq-PCA.pptx -------------------------------------------------------------------------------- /Lectures/B9.b_HPC.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuLab/Applied-Bioinformatics/7c01300871e64c09fec7ade1af4c2f3c8bb074e5/Lectures/B9.b_HPC.pptx -------------------------------------------------------------------------------- /Lectures/C10.a_Capstone-a.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuLab/Applied-Bioinformatics/7c01300871e64c09fec7ade1af4c2f3c8bb074e5/Lectures/C10.a_Capstone-a.pptx -------------------------------------------------------------------------------- /Lectures/C10.b_Capstone-b.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuLab/Applied-Bioinformatics/7c01300871e64c09fec7ade1af4c2f3c8bb074e5/Lectures/C10.b_Capstone-b.pptx -------------------------------------------------------------------------------- /Lectures/C11.a_InvitedTalks-BioinformaticsResearch.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuLab/Applied-Bioinformatics/7c01300871e64c09fec7ade1af4c2f3c8bb074e5/Lectures/C11.a_InvitedTalks-BioinformaticsResearch.pptx -------------------------------------------------------------------------------- /Lectures/C11.b_TSRI-BioinformaticsPanel.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SuLab/Applied-Bioinformatics/7c01300871e64c09fec7ade1af4c2f3c8bb074e5/Lectures/C11.b_TSRI-BioinformaticsPanel.pptx -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Applied Bioinformatics 2 | Welcome to the Applied Bioinformatics course offered at [The Scripps Research Institute](https://www.scripps.edu/). 3 | 4 | Instructors: Dr. Andrew I Su ([@andrewsu](https://github.com/andrewsu))
5 | Teaching Assistants (TAs): 6 | * Kai-Yu Chen ([@chvbs2000](https://github.com/chvbs2000)) 7 | * Carolina Gonzalez ([@Carolina1396](https://github.com/Carolina1396)) 8 | * Shashank Nagaraja ([@dapluggg](https://github.com/dapluggg)) 9 | * Roger Tu ([@turoger](https://github.com/turoger)) 10 | 11 | This course is available in 2 parts and operates under the Computational Biology & Bioinformatics (CBB) core track: 12 | 13 | * Fundamentals of Scientific Computing, 4 weeks (1 credit)
14 | 1. Learn how to use RStudio and R 15 | 2. Learn basics of data visualization and exploratory data analysis 16 | 3. Learn to use R Notebooks 17 | 18 | * Applied Bioinformatics and Computational Biology (ABCB), 8 weeks (2 credits) 19 | 1. Learn the fundamentals of exploratory analysis of RNA-seq data, including PCA and clustering 20 | 2. Learn the fundamentals of differential expression analysis, enrichment analysis, and visualization 21 | 3. Practice and present on learned R skillset through published data via Capstone project. 22 | 23 | ## Prerequisites 24 | * A recent computer running Windows 10/11, MacOS, or Linux (inform instructors if you have any concerns) 25 | * Software installation prior to first class ([instructions](Configuration.md)) 26 | 27 | 28 | ## Course Materials 29 | 30 | This section will be updated as the course progresses. 31 | 32 | * Tuesday 2022-09-06: Course intro 33 | * [slides](https://docs.google.com/presentation/d/1Ye8nBg-IsF0laGGY8Lf78Nd8CMAGkYft/edit?usp=sharing) 34 | * Homework due Monday 2022-09-12 3PM PT 35 | * Thursday 2022-09-08: Data visualization 36 | * [slides](https://docs.google.com/presentation/d/16JYUXOdfllGqmlcu31UCj_EvJO38pytOx26DsmToSMo/edit?usp=sharing) 37 | * Homework due Monday 2022-09-19 3PM PT 38 | * Tuesday 2022-09-13: 39 | * [slides](https://docs.google.com/presentation/d/1_AXs9embC_X9mpBgL7Bt-ddY5_UgbMt2eKLVm4_BEkY/edit?usp=sharing) 40 | * Homework due Monday 2022-09-19 3PM PT 41 | * Thursday 2022-09-15: 42 | * slides (to be posted) 43 | * Homework due Monday 2022-09-26 3PM PT 44 | 45 | Credit to past instructors and TAs: Dr. Sabah Ul-Hasan ([@sabahzero](https://github.com/sabahzero)), Dr. Huitian Yolanda Diao ([@Huitian](https://github.com/Yolanda-HT)), Dr. Karthik Gangavarapu ([@gkarthik](https://github.com/gkarthik)), Shang-Fu Chen ([@ShaunFChen](https://github.com/ShaunFChen)), Jerry Zak ([@trebbiano](https://github.com/trebbiano)) 46 | -------------------------------------------------------------------------------- /git-installation.md: -------------------------------------------------------------------------------- 1 | # Installing git 2 | 3 | You will be following the links and instructions at https://git-scm.com/downloads 4 | 5 | ## MacOs 6 | * follow the "homebrew" instructions, which boil down to executing these two commands in your Terminal application: 7 | * `/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"` 8 | * `brew install git` 9 | 10 | ## Ubuntu Linux 11 | * Execute `apt-get install git`. If you see any errors, try `sudo apt-get install git`. 12 | 13 | ## Windows 14 | * The installer will ask you what you'd like to make the default editor. Unless you know the difference between the different options, select "Nano" 15 | * Select the "Override the default branch name for new repositories" option. Leave the default of "main". 16 | * Choose all other defaults. 17 | 18 | # Configuring git in RStudio 19 | * Installation instructions are derived from [Computing for Social Sciences at The University of Chicago](https://cfss.uchicago.edu/setup/what-is-git/ "Computing for Social Sciences at The University of Chicago") and [happy git with R](https://happygitwithr.com/https-pat.html). 20 | * There are two methods of communicating with your remote repository on github using RStudio. One uses Personalized Access tokens (PAT) and the other uses Secure Shell (SSH). The choice is up to you. 21 | * Most recommend configuring PAT as it is easier to get working quickly. Simply generate a token and provide the token next time a Git operation asks for your password. To follow a PAT protocol you need to clone a repository using the `HTTPS` link which usually follows the pattern `https://github.com//.git`. You can get this link from the `Code` button in your GitHub repository. 22 | * SSH comes in handy when you're working with servers and is generally more secure. Unlike using HTTPS, you do not need to generate a new PAT monthly. To follow a SSH protocol you clone a repository using the `SSH` link whcih follows the pattern `git@github.com:/.git`. 23 | 24 | ## Configuring PAT 25 | * Go to [https://github.com/settings/tokens](https://github.com/settings/tokens) and select "Generate new token". 26 | * Select "repo", "workflow", and "user". 27 | * In RStudio Console, copy your PAT from GitHub and paste your PAT into the console after calling: 28 | 29 | ```R 30 | install.packages(c("usethis", "gitcreds", "gh")) 31 | gitcreds::gitcreds_set() 32 | ``` 33 | 34 | ## Configuring SSH 35 | 36 | * Tell R who you are: 37 | * `user.name` can be your real name ('First', 'Last') or your github username 38 | * `user.email` needs to be your github email address 39 | 40 | ```R 41 | usethis::use_git_config(user.name = "Your Name", user.email = "youremail@scripps.edu") 42 | ``` 43 | 44 | * create a SSH key by running the following command in R console: 45 | * allows you to push updates to github without typing in your password 46 | * Click 'yes' when prompted to generate a new SSH key 47 | 48 | ```R 49 | credentials::ssh_setup_github() 50 | ``` 51 | 52 | * Configure github by pasting your key into your account. 53 | * When prompted to open your browser to paste your key into github, click yes 54 | * Name your key in `Title`. You can label it whatever you want. I named mine "RStudio" 55 | * Paste your public key to github and click "Add SSH key" 56 | 57 | ## Creating a repository for your RProject 58 | * There are a couple methods to create a repository (repo). (1) You can create a repo online using GitHub. (2) You can create a repo using Terminal on your computer and sync it to your GitHub. Either way, you need to login to GitHub and create a 'new' repository. This can be done [here](https://github.com/new). Make sure when you copy and paste your remote repo location, select the SSH hyperlink. 59 | 60 | ### Creating a repo online using GitHub and push to it 61 | * Navigate to where you want to pull your remote repository to in Terminal. I'm using fluffy-octo-journey as my repo in this example. 62 | 63 | ```bash 64 | git remote add origin git@github.com:turoger/fluffy-octo-journey.git 65 | git branch -M main 66 | git push -u origin main 67 | ``` 68 | 69 | ### Creating a repo locally using Terminal and push to remote GitHub 70 | * Navigate to where your project files are in Terminal 71 | Initialize git and add it to your remote repository on GitHub. I'm using fluffy-octo-journey as my repo in this example. 72 | 73 | ```bash 74 | git init 75 | git commit -m "First commit to GitHub for my RProject" 76 | git remote add origin 77 | git branch -M main 78 | git remote add origin git@github.com:turoger/fluffy-octo-journey.git 79 | git push -u origin main 80 | ``` 81 | --------------------------------------------------------------------------------