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    "# Bioinformatics Table of Contents\n",
    "\n",
    "<!---\n",
    "### Lecture Slides\n",
    "* \n",
    "\n",
    "#### TODO\n",
    "* Add intro text to each notebooks with overview of what it will cover\n",
    "* add in md5sum discussion (in QC?)\n",
    "\n",
    "\n",
    "data_provenance.ipynb\n",
    "quality_scores.ipynb\n",
    "-->\n",
    "\n",
    "\n",
    "## Week 2, Day 5 (7/13/2018)\n",
    "1. [Lecture Slides: Lab Followup](../slides/0713_lab_followup.pdf)\n",
    "1. [Lecture Slides: Bioinformatics Pipeline](../slides/0713_bioinformatics_overview.pdf)\n",
    "1. [Introduction to FASTQs](fastq_intro.ipynb)\n",
    "    * [Quality Scores](quality_scores.ipynb)\n",
    "1. [Quality Control](fastqc.ipynb)\n",
    "1. [Trimming and Filtering](fastq_trimming.ipynb)\n",
    "1. [Download and Index Genome](genome_prep.ipynb)\n",
    "1. [Mapping Reads to a Reference Genome](mapping.ipynb)\n",
    "1. [Hands On Exercise #1](bioinf_hands_on_1.ipynb) \n",
    "\n",
    "## Week 4, Day 1 (7/23/2018)\n",
    "1. [Counting Reads](counting.ipynb)\n",
    "1. [Working with Paired Reads](paired_data_pipeline.ipynb)\n",
    "1. [Making Generic Commands](making_generic_commands.ipynb)\n",
    "1. [Making a Pipeline](making_a_pipeline.ipynb)\n",
    "1. [Pipeline in a Loop](loop_pipeline.ipynb)\n",
    "1. [Running Multiple FASTQs](multifastq_loop_pipeline.ipynb)\n",
    "1. [Looping with Globs](glob_loop.ipynb)\n",
    "1. [Hands On Exercise #2](bioinf_hands_on_2.ipynb) \n",
    "\n",
    "## Week 4, Day 2 (7/24/2018)\n",
    "* [IGV visualization](igv_visualization.ipynb)\n",
    "    * [Shorter Introns](igv_shorter_introns.ipynb)\n",
    "1. [Hands On Exercise #3](bioinf_hands_on_3.ipynb) \n",
    "\n",
    "\n",
    "## Appendix\n",
    "* [Demultiplex Raw FASTQs](demultiplex.ipynb)\n",
    "* [Bash Functions](bash_functions.ipynb)\n",
    "\n",
    "<!---\n",
    "\n",
    "1. [Pipeline with Loops](filled_nb/loop_pipeline.ipynb) ([clean notebook](clean_nb/loop_pipeline_clean.ipynb))\n",
    "1. [Pipeline for Multiple Samples](filled_nb/full_pilot_data_pipeline.ipynb) ([clean notebook](clean_nb/full_pilot_data_pipeline_clean.ipynb))\n",
    "\n",
    "## Pipeline for All 2015 Data\n",
    "\n",
    "1. [Demultiplex All 2015 Data](filled_nb/full_2015_data_demux.ipynb)\n",
    "1. [Demuxed FASTQ to Counts for All 2015 Data](filled_nb/full_2015_data_pipeline.ipynb)\n",
    "\n",
    "* [Using Bash in a Python Notebook](filled_nb/bash_magic.ipynb)\n",
    "\n",
    "## Parallelize\n",
    "* https://unix.stackexchange.com/questions/103920/parallelize-a-bash-for-loop\n",
    "* https://stackoverflow.com/questions/38160/parallelize-bash-script-with-maximum-number-of-processes\n",
    "* https://stackoverflow.com/questions/38774355/how-to-parallelize-for-loop-in-bash-limiting-number-of-processes\n",
    "-->\n",
    "\n",
    "<!---\n",
    "\n",
    "## Bonus\n",
    "* [Does Filtering Matter? Mapping unfiltered paired reads](filled_nb/paired_pilot_data_pipeline_unfiltered.ipynb)\n",
    "1. [demux_exploration](filled_nb/demux_exploration.ipynb) ([clean notebook](clean_nb/demux_exploration_clean.ipynb))\n",
    "1. [working_with_your_data](filled_nb/working_with_your_data.ipynb) ([clean notebook](clean_nb/working_with_your_data_clean.ipynb))\n",
    "\n",
    "#### Bioinformatics Pipeline on Full Dataset\n",
    "\n",
    "\n",
    "-->"
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