[Statlist] BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS - Workshop

[oiiverhooker m@iii@g oii prst@tistics@co@uk]

BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS - Workshop - 19th - 23rd October 2015
The handling of large data-sets has become intractable without some level of bioinformatic literacy. Many biologists find that there is a steep learning curve to develop the confidence required to explore their genomics data-sets effectively. This bioinformatics short course includes a rich collection of hands-on instruction and lectures specifically intended to help novice users become comfortable with a range of tools currently used to analyse next-generation data. There is no prerequisite for this course other than a willingness to learn and to work hard throughout the week.
The course will be held at SCENE (Scottish Center for Ecology and the Natural Environment), Glasgow, United Kingdom and will be delivered by Dr Nic Blouin and Dr Ian Misner.
The course is 5 days long and will have a day spent on each of the following; Linux, RNAseq, Assembly, Annotation and Python, more details on each of these day long modules and the course can be found at<http://prstatistics.co.uk/bioinformatics%20for%20biologists/index.html>
Course timetable
Day 1: Linux
Linux is taught on the first day, this takes the entire day. Once you get through this portion you will be on your way to completing your own NGS analysis. We have created a workbook for this portion of the course. This is a step by step, or in the case, command-by-command, Linux guide. We complete each command as a class and discuss and review issues along the way.
Day 2: RNAseq
We will cover two of the more popular tools in this workshop, The Tuxedo package & Trinity. Outcomes: confidence to design effective RNAseq experiments; knowledge of NGS sequencing platforms and their differing applications, ability to analyze Illumina data for quality and contamination; proficiency to implement the Tuxedo package to analyze an RNAseq dataset; create publication ready graphics with cummeRbund and EdgeR.
Day 3: Assembly
Whether you have a reference genome or are working with de novo samples there are some basic tools and practices that we cover to help assist you in your genome project. In this module we will cover the basic metrics you should review when doing assembly as well as best practices to consider in your own project. Outcomes: take raw reads through a complete assembly process; working knowledge of different assembly issues/challenges; the effect of assembly settings on assembly outcomes.
Day 4: Annotation
We will use MAKER and Blast2GO and annotate the genome we assembled in the assembly module.
Outcomes: understand the differences between functional and structural annotations; train MAKER to improve structural annotations; understand how MAKER improves with more evidence and training; visualize structural annotations; apply functional annotations with Blast2GO.
Day 5: Python
Why Python? In truth it doesn’t matter what coding language you learn but you should learn one. Python has a very straightforward syntax that is easy to understand. In this module we will utilize the clearly explained training examples from Python for Biologists. Outcomes: understand Python language syntax; create scripts to answer biological problems & parse and analyze BLAST outputs using custom Python code.
Costs start at £540 course only and includes lunches and refreshments or £715.00 for an all-inclusive option which includes all accommodation and meals full pricing and details on accommodation can be found via the website.
For further details or questions please visit www.prstatistics.co.uk or email oliverhooker using prstatistics.co.uk
Please feel free to distribute this information among friends and colleagues where suitable
Other upcoming courses include; ANALYSIS OF STABLE ISOTOPE DATA USING SIA-R; GENETIC DATA ANALYSIS IN R; APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS; SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R; ADVANCING IN R; further details on all of these can be found at www.prstatistics.co.ukOliver Hooker
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