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Bioinformatics for geneticists and biologists (BIGB02)
3rd July 2017 - 7th July 2017£260.00 - £620.00
The handling of large datasets 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 datasets 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.
The course is aimed at anyone interested in learning bioinformatics tools needed for handling large genomic datasets.
We offer COURSE ONLY and ACCOMMODATION PACKAGES;
• COURSE ONLY – Includes lunch and refreshments.
• ACCOMMODATION PACKAGE (to be purchased in addition to the course only option) – Includes breakfast, lunch, dinner, refreshments, minibus to and from meeting point and accommodation. Accommodation is multiple occupancy (max 3 people) single sex en-suite rooms. Arrival Sunday 2nd July PM and departure Friday 7th July PM.
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Cancellation policy: Cancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered, contact firstname.lastname@example.org Failure to attend will result in the full cost of the course being charged. In the unfortunate event that PRinformatics must cancel this course due to unforeseen circumstances a full refund for the course will be credited. However PRinformatics cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.
Dr. Ian Misner
This is principally a hands-on course. Participants will conduct all analyses in this course using their own laptops. Introductory lectures on the concepts will be given as necessary.
Assumed quantitative knowledge
There is no prerequisite quantitative knowledge to benefit from this course.
Assumed computer background
There is no prerequisite computer knowledge to benefit from this course. This course is aimed at beginners and for those who have some introduction to working on the command line, but lack confidence to perform analysis on large datasets and parse output data.
Equipment and software requirements
A laptop/personal computer with 4gb RAM (8gb is optimal), 60gb free space on hard drive computer.
It is essential that you come with all necessary software and packages already installed (you will be sent a list of packages prior to the course) internet access may not always be available.
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Meet at the Tullie Inn, Balloch at approximately 18:30 before being taken by minibus to SCENE (Download directions PDF).
Monday 3rd – Classes from 09:00 to 17:00
Module 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.
Tuesday 4th – Classes from 09:00 to 17:00
Module 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.
Wednesday 5th – Classes from 09:00 to 17:00
Module 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.
Thursday 6th – Classes from 09:00 to 17:00
Module 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.
Friday 7th – Classes from 09:00 to 16:00
Module 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 utilise the clearly explained training examples from Python for Biologists. Outcomes; Understand Python language syntax. Create scripts to answer biological problems & parse and analyse BLAST outputs using custom Python code.