search_index.json

[
["index.html", "16s rRNA analysis workshop 1 Introduction 1.1 Workshop Schedule 1.2 Important links", " 16s rRNA analysis workshop Hena R. Ramay 2019-10-06 1 Introduction Our intention is to develop workshop material as we go along. For each day of the workshop, the basic material will be uploaded and more details will be added based on your questions and problems we encounter. So pleae ask as many questions are you can to help us in making this workshop better!! 1.1 Workshop Schedule We will try to cover the following material in the course: Day1 9:30 - 10:30 am Introductions and a presentation of the basic concepts 10:30 - 10:45 am Break 10:45 - 12 pm Installations of the required packages and data download 12 - 1 pm Lunch break 1 - 3 pm Reading data in and inspecting read quality Day2 9:30 -10:30 am Filter and trim + learn error rates + Sample inference + Merge samples 10:30 - 10:45 am Break 10:45 - 12 Generate sequence table and remove Chimeras 12 - 1 pm Lunch break 1- 3 pm Taxomnomy explanation + assign your sequences. If time permits, make a phyloseq object Day3 9-10:30 am Using a phyloseq object to calculate alpha and beta diversity 10:30 onwards we will use a real world dataset to re-do what we have learned here 1.2 Important links DADA2 Tutorial : link Day One presentaton : link Day One dataset : link "],
["day-one.html", "2 Day One 2.1 What are we trying to achieve 2.2 Basics & Background 2.3 DADA2 pipeline (v1.2) 2.4 Inspect read quality profiles", " 2 Day One We are very excited to teach this course for the first time and share what we know with you all So lets start by talking about the very basics: 2.1 What are we trying to achieve Our goal is very similar to gathering data on a city neighbourhood to find out who lives there, how the demographic changes over time or in case of a drastic event. We can gather more information by asking about neighbours, quality of life etc. Similarly when we are looking at microbial communities our first question is who is there, how abundant and how their presence changes over time or when conditions change. We can also ask questions like how the microbiomes are interacting with each other (metabolites). For the scope of this workshop we will stick to the simple questions: who and how much? 2.2 Basics & Background Here is the link to the lecture we will start with today: workshop Key points are: Think of a hypothesis before doing an experiment Spend time on experiment design. Sample size, 16s region to amplify etc Talk to a bioinformatician Think about the depth of sequencing if you want to capture the less abundant taxa Add negative control to account for contamination Thoughtful data analysis is critical for successful identification of microbes “If you torture the data long enough, it will confess.”- Ronald Coase, Economist 2.3 DADA2 pipeline (v1.2) From now on, we will be working on the DADA2 package version 1.12. DADA2 has great documentation and an excellent tutorial online that we will use to understand the pipeline. Please go to the following link http://benjjneb.github.io/dada2/tutorial.html 2.3.1 Data for the tutorial The data to use for the tutorial can be downloaded from here 2.3.2 Getting ready ( load packages and get file list) functions that we will be using here are : list.files() sort() strsplit() basename() sapply() 2.4 Inspect read quality profiles "],
["day-two.html", "3 Day Two", " 3 Day Two We describe our methods in this chapter. "],
["day-three.html", "4 Day Three", " 4 Day Three "],
["summary.html", "5 Summary", " 5 Summary "],
["references.html", "References", " References "]
]