Merge pull request #53 from jacquikeane/fix_typos

Minor updates and fixed typos

Notebooks/ARIBA/index.ipynb

@@ -15,7 +15,7 @@
  "> PMID: [29177089](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5695208/) \n",
  "\n",
  "## Learning outcomes\n",
- "By the end of this tutorial you will be able to:\n",
+ "By the end of this tutorial you can expect to be able to:\n",
  "\n",
  "* Download and prepare the standard AMR databases for use with ARIBA\n",
  "* Prepare your own database for use with ARIBA\n",
@@ -28,7 +28,7 @@
  "\n",
  "\n",
  "## Tutorial sections\n",
- "This tutorial comprises the following stages:\n",
+ "This tutorial comprises the following sections:\n",
  "\n",
  "1. [How to use custom reference data with ARIBA](make_custom_db.ipynb)\n",
  "2. [Run ARIBA using the custom reference data](run_ariba.ipynb)\n",
@@ -72,7 +72,7 @@
  "metadata": {},
  "source": [
  "### Running commands in the terminal\n",
- "You can also follow this course by typing all the commands you see into a terminal window. This is similar to the \"Command Prompt\" window on MS Windows systems, which allows the user to type DOS commands to manage files.\n",
+ "You can also follow this tutorial by typing all the commands you see into a terminal window. This is similar to the \"Command Prompt\" window on MS Windows systems, which allows the user to type DOS commands to manage files.\n",
  "\n",
  "To get started, select the cell below with the mouse and then either press control and enter or choose Cell -> Run in the menu at the top of the page."
  ]

Notebooks/BLAST/index.ipynb

@@ -23,10 +23,10 @@
  "Why do I need this tutorial you may say! Well, running BLAST+ is like running a lab experiment. To get meaningful results, you must first optimize the conditions you are using. After this tutorial you will not only be able to run BLAST, but be able to tailor your search to your specific biological question.\n",
  "\n",
  "## Learning outcomes\n",
- "By the end of this tutorial you will be able to:\n",
+ "By the end of this tutorial you can expect to be able to:\n",
  "\n",
  "* Create a BLAST database from your own sequences\n",
- "* Understand the difference between BLAST programs and when to use them\n",
+ "* Describe the difference between BLAST programs and when to use them\n",
  "* Run BLAST locally\n",
  "* Generate tailored BLAST output files \n",
  "\n",
@@ -69,7 +69,7 @@
  "metadata": {},
  "source": [
  "### Running commands in the terminal\n",
- "You can also follow this course by typing all the commands you see into a terminal window. This is similar to the \"Command Prompt\" window on MS Windows systems, which allows the user to type DOS commands to manage files.\n",
+ "You can also follow this tutorial by typing all the commands you see into a terminal window. This is similar to the \"Command Prompt\" window on MS Windows systems, which allows the user to type DOS commands to manage files.\n",
  "\n",
  "To get started, select the cell below with the mouse and then either press control and enter or choose Cell -> Run in the menu at the top of the page."
  ]

Notebooks/IGV/index.ipynb

@@ -4,7 +4,8 @@
  "cell_type": "markdown",
  "metadata": {},
  "source": [
- "# Introduction to Integrated Genome Viewer (IGV)"
+ "# Introduction to Integrated Genome Viewer (IGV)\n",
+ "## A quick start guide"
  ]
  },
  {
@@ -27,7 +28,7 @@
  "source": [
  "## Learning outcomes\n",
  "\n",
- "By the end of this quick start guide you will be able to:\n",
+ "By the end of this quick start guide you can expect to be able to:\n",
  "\n",
  " * Index a reference genome for IGV\n",
  " * Load a reference genome file into IGV\n",

Notebooks/QC/assessment.ipynb

@@ -77,9 +77,7 @@
  "``` \n",
  "data/lane1/s_7_1.fastq \n",
  "data/lane1/s_7_2.fastq \n",
- "```\n",
- "\n",
- "You can test your check in the code window below:"
+ "```"
  ]
  },
  {

Notebooks/QC/contamination.ipynb

@@ -92,8 +92,20 @@
  "\n",
  "__Q1: What is the most prevalent species in this sample? \n",
  "Q2: Are there clear signs of contamination? \n",
- "Q3: What percentage of reads could not be classified?__ \n",
- "\n",
+ "Q3: What percentage of reads could not be classified?__ "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
  "Congratulations! You have reached the end of this tutorial. You can find the answers to all the questions of the tutorial [here](answers.ipynb). \n",
  "To revisit the previous section [click here](assessment.ipynb). Alternatively you can head back to the [index page](index.ipynb)"
  ]

Notebooks/QC/formats.ipynb

@@ -87,7 +87,7 @@
  "cell_type": "markdown",
  "metadata": {},
  "source": [
- "### Excercises\n",
+ "### Exercises\n",
  "\n",
  "From reading section 1.3 of the SAM specification, look at the following line from the header of the SAM/BAM file: \n",
  "\n",
@@ -205,7 +205,7 @@
  "cell_type": "markdown",
  "metadata": {},
  "source": [
- "### Excercises\n",
+ "### Exercises\n",
  " \n",
  "Samtools comprises a set of programs for interacting with SAM and BAM files. Using the samtools view command, print the header of the BAM file:"
  ]

Notebooks/QC/index.ipynb

@@ -7,7 +7,7 @@
  "# NGS Data formats and QC\n",
  "\n",
  "## Introduction\n",
- "There are several file formats for storing Next Generation Sequencing (NGS) data. In this tutolial we will look at some of the most common file formats for storing NGS reads and variant data. We will cover the following formats:\n",
+ "There are several file formats for storing Next Generation Sequencing (NGS) data. In this tutolial we will look at some of the most common formats for storing NGS reads and variant data. We will cover the following formats:\n",
  "\n",
  "__FASTQ__ - This format stores unaligned read sequences with base qualities \n",
  "__SAM/BAM__ - This format stores unaligned or aligned reads (text and binary formats) \n",
@@ -16,7 +16,7 @@
  "\n",
  "Following this, we will work through some examples of converting beween the different formats. \n",
  "\n",
- "Further to understanding the differenet fie formats, it is important to remember that all sequencing platforms have technical limitations that can introduce biases in your sequencing data. Because of this it is very important to check the quality of the data before starting any analysis, whether you are planning to use something you have sequenced yourself or publicly available data. In the altter part of this tutorial we wil describe how to perform a QC assessment for your NGS data, and also siuggest how to identify possible contamination.\n",
+ "Further to understanding the differenet fie formats, it is important to remember that all sequencing platforms have technical limitations that can introduce biases in your sequencing data. Because of this it is very important to check the quality of the data before starting any analysis, whether you are planning to use something you have sequenced yourself or publicly available data. In the latter part of this tutorial we wil describe how to perform a QC assessment for your NGS data, and also suggest how to identify possible contamination.\n",
  "\n",
  "## Learning outcomes\n",
  "On completion of the tutorial, you can expect to be able to:\n",
@@ -27,7 +27,7 @@
  "* Identify possible contamination in high throughput sequence data\n",
  "\n",
  "## Tutorial sections\n",
- "This tutorial comprises the following stages:\n",
+ "This tutorial comprises the following sections:\n",
  "1. [Data formats](formats.ipynb)\n",
  "2. [File conversion](conversion.ipynb)\n",
  "3. [QC assessment](assessment.ipynb)\n",
@@ -66,7 +66,7 @@
  "metadata": {},
  "source": [
  "### Running commands in the terminal\n",
- "You can also follow this course by typing all the commands you see into a terminal window. This is similar to the \"Command Prompt\" window on MS Windows systems, which allows the user to type DOS commands to manage files.\n",
+ "You can also follow this tutorial by typing all the commands you see into a terminal window. This is similar to the \"Command Prompt\" window on MS Windows systems, which allows the user to type DOS commands to manage files.\n",
  "\n",
  "To get started, select the cell below with the mouse and then either press control and enter or choose Cell -> Run in the menu at the top of the page."
  ]

Notebooks/RNA-Seq/index.ipynb

@@ -33,7 +33,7 @@
  "source": [
  "## Learning outcomes\n",
  "\n",
- "By the end of this tutorial you will be able to: \n",
+ "By the end of this tutorial you can expect to be able to: \n",
  "\n",
  " * Align RNA-Seq reads to a reference genome and a transcriptome \n",
  " * Visualise transcription data using standard tools \n",
@@ -46,7 +46,7 @@
  "metadata": {},
  "source": [
  "## Tutorial sections\n",
- "This tutorial comprises the following stages: \n",
+ "This tutorial comprises the following sections: \n",
  "\n",
  " 1. [Introducing the tutorial dataset](dataset-intro.ipynb) \n",
  " 2. [Mapping RNA-Seq reads to the genome with HISAT2](genome-mapping.ipynb) \n",
@@ -105,7 +105,7 @@
  "metadata": {},
  "source": [
  "### Running commands in the terminal\n",
- "You can also follow this course by typing all the commands you see into a terminal window. This is similar to the \"Command Prompt\" window on MS Windows systems, which allows the user to type DOS commands to manage files.\n",
+ "You can also follow this tutorial by typing all the commands you see into a terminal window. This is similar to the \"Command Prompt\" window on MS Windows systems, which allows the user to type DOS commands to manage files.\n",
  "\n",
  "To get started, select the cell below with the mouse and then either press control and enter or choose Cell -> Run in the menu at the top of the page. "
  ]

Notebooks/ROARY/index.ipynb

@@ -18,19 +18,19 @@
  "or visit the [Roary manual](http://sanger-pathogens.github.io/Roary/).\n",
  "\n",
  "## Learning outcomes\n",
- "By the end of this tutorial you will be able to:\n",
+ "By the end of this tutorial you can expect to be able to:\n",
  "\n",
- "* Understand what a pan genome is\n",
+ "* Describe what a pangenome is\n",
  "* Prepare data for input to Roary\n",
  "* Perform QC on input data and understand why QC is important\n",
- "* Run Roary to create a pan genome with and without a core alignment \n",
+ "* Run Roary to create a pangenome with and without a core alignment \n",
  "* Understand the different output files produced by Roary\n",
  "* Draw a basic tree from the core gene alignment produced by Roary\n",
  "* Query the pangenome results produced by Roary\n",
  "* Use Phandango to visualise the results produced by Roary \n",
  "\n",
  "## Tutorial sections\n",
- "This tutorial comprises the following stages:\n",
+ "This tutorial comprises the following sections:\n",
  "1. [What is a pan genome](pan_genome.ipynb)\n",
  "2. [Preparing the input data](prepare_data.ipynb)\n",
  "3. [Performing QC on your data](qc.ipynb)\n",
@@ -75,7 +75,7 @@
  "metadata": {},
  "source": [
  "### Running commands in the terminal\n",
- "You can also follow this course by typing all the commands you see into a terminal window. This is similar to the \"Command Prompt\" window on MS Windows systems, which allows the user to type DOS commands to manage files.\n",
+ "You can also follow this tutorial by typing all the commands you see into a terminal window. This is similar to the \"Command Prompt\" window on MS Windows systems, which allows the user to type DOS commands to manage files.\n",
  "\n",
  "To get started, select the cell below with the mouse and then either press control and enter or choose Cell -> Run in the menu at the top of the page."
  ]

Notebooks/SEROBA/index.ipynb

@@ -16,7 +16,7 @@
  "> _bioRxiv preprint, 2017 Sep.; doi: [10.1101/179465](https://www.biorxiv.org/content/early/2017/09/05/179465)_\n",
  "\n",
  "## Learning outcomes\n",
- "By the end of this tutorial you will be able to:\n",
+ "By the end of this tutorial you can expect to be able to:\n",
  "\n",
  "* Understand serotyping, why it is important and what it can be used for\n",
  "* Run SeroBA on several samples to predict their serotype\n",
@@ -25,7 +25,7 @@
  "* Download and prepare the S. pneumoniae databases from PneumoCAT for use with SeroBA\n",
  "\n",
  "## Tutorial sections\n",
- "This tutorial comprises the following stages:\n",
+ "This tutorial comprises the following sections:\n",
  "\n",
  "1. [What is serotyping?](serotyping.ipynb)\n",
  "2. [Preparation of databases before running SeroBA](db_setup.ipynb)\n",
@@ -69,7 +69,7 @@
  "metadata": {},
  "source": [
  "### Running commands in the terminal\n",
- "You can also follow this course by typing all the commands you see into a terminal window. This is similar to the \"Command Prompt\" window on MS Windows systems, which allows the user to type DOS commands to manage files.\n",
+ "You can also follow this tutorial by typing all the commands you see into a terminal window. This is similar to the \"Command Prompt\" window on MS Windows systems, which allows the user to type DOS commands to manage files.\n",
  "\n",
  "To get started, select the cell below with the mouse and then either press control and enter or choose Cell -> Run in the menu at the top of the page."
  ]