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Old 11-22-2014, 10:46 AM   #1
ecSeq Bioinformatics
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Exclamation Upcoming NGS Workshop: A Beginner's Guide to NGS Data Analysis (early march 2015)

A Beginner's Guide to NGS Data Analysis
Quality Control, Read Mapping, Visualization and Downstream Analyses

When?
9. - 13. March 2015

Where?
Leipzig, Germany

Scope and Topics
The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Additionally, all workshop participants should be enabled to perform important tasks of NGS data analysis tasks themselves.

The first workshop module is an introduction to data analysis using Linux, assuring that all participants are able to follow the practical parts. The second module dicusses advantages and disadvantages of current sequencing technologies and their implications on data analysis. The most important NGS file formats (fastq, sam/bam, bigWig, etc.) are introduced and one proceeds with first hands-on analyses (QC, mapping, visualization). You will learn how to read and interprete QC plots, clip adapter sequences and/or trim bad quality read ends, get bioinformatics backgrounds about the read mapping and understand its problems (dynamic programming, alignment visualization, NGS mapping heuristics, etc.), perform your own mapping statistics and visualize your data in different ways (IGV, UCSC, etc.). The last two modules adress two specific applications of NGS: RNA-seq of model organisms and RNA-seq of non-model organisms.

Workshop Structure
The 2015 workshop has been redesigned and adapted to the needs of beginners in the field of NGS bioinformatics. The worshops comprises four course modules which can be combined.

Linux for Bioinformatics:
This course module is optional. It will introduce the essential tools and file formats required for NGS data analysis. It helps to overcome the first hurdles when entering this (for NGS analyses) unavoidable operating system. Every participant who has no background in Linux usage should attend this course!
(The linux calls and commandline pipes teached here are the basis for all other courses and can not be covered again!)
Introduction to NGS data analysis:
This module is mandatory. Different methods of NGS will be explained, the most important notations be given and first analyses be performed. This course covers essential knowledge for analysing data of many different NGS applications. It also assures that all participants will be on the same level of knowledge for the downstream courses.
RNA-seq Data Analyses:
Particpants can choose up to one of the following options:
  1. RNA-Seq for model-organisms
  2. RNA-Seq for non-model organisms
Depending on the organism you are working with, our trainers will show you what's possible with your data and how you could/should interprete the output data.

Key Dates
Opening Date of Registration: 10 November 2014
Closing Date of Early Registration: 15 January 2015
Closing Date of Registration: 1 March 2015
Workshop: 9 - 13 March 2015 (8 am - 5 pm)

Attendance
Location: iad Pc-Pool, Rosa-Luxemburg-Straße 23, Leipzig, Germany
Language: English
Available seats: 24 (first-come, first-served)

Course Prices and Program
The prices and the program can be found on our workshop website:
http://www.ecseq.com/workshops/workshop_2015-01.html

Contact
ecSeq Bioinformatics
Brandvorwerkstr.43
04275 Leipzig
Germany
Web: www.ecseq.com
Email: [email protected]
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Old 11-22-2014, 11:17 AM   #2
Brian Bushnell
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I would be happy to fly over and train people on the use of BBTools for QC, mapping, and visualization, if you're interested. They're free, and optimal in many areas.
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Old 11-22-2014, 12:56 PM   #3
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Quote:
Originally Posted by Brian Bushnell View Post
I would be happy to fly over and train people on the use of BBTools for QC, mapping, and visualization, if you're interested. They're free, and optimal in many areas.
Thanks for the offer, Brian. I use BBDuk from the BBTools and it is a really great tool. Nevertheless, for our courses we we do not want to highlight one tool/toolkit, but we want to give an overview of several tools and train the participants in understanding the differences and finally choosing the correct one for their project.

We previously did some courses completely depending on one toolkit, but we realized that these events (as you said) have to be free of charge, otherwise they are too much of a promotional event. Our goal is to show researchers what they can do and how they can do it (in different ways). I highly believe that there is not one single tool/pipeline for all experiments. Every experiment on its own has to be analyzed in an appropriate/specialized way. That's what we try to teach.

But we will add some tools from BBtools from which we believe they are worth a try for our participants (e.g. BBDuk).
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Old 11-22-2014, 01:00 PM   #4
Brian Bushnell
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Quote:
Originally Posted by ecSeq Bioinformatics View Post
I highly believe that there is not one single tool/pipeline for all experiments. Every experiment on its own has to be analyzed in an appropriate/specialized way. That's what we try to teach.
I completely agree with your philosophy. Thanks for your reply!
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Old 12-15-2014, 04:05 AM   #5
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UPDATE: The course for next year fills up unexpectedly fast.

I just want to mention that here, since we got several emails asking if there are still some seats available. I can tell you that there are some seats available for the course above. But, if you cannot apply now and thus will be too late to catch a seat, you can try to apply for our other (2-days) course in Oxford: http://lpmhealthcare.com/ngs-workshop-2015-oxford/
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Old 12-19-2014, 02:27 AM   #6
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UPDATE: We just closed the registration for the 'non-model organism' downstream module.

The application for the 'model-organism' module is still open.
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Old 01-11-2015, 09:48 PM   #7
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Early Bird Registration Deadline ending soon!

I kindly want to remind you that the period of the early bird registration for our workshop 'A Beginner's Guide to NGS Data Analysis' is ending soon. Don’t miss the chance to register during the time with the most favourable conditions. After January 15th the prices will increase by 10%.
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Old 01-14-2015, 11:57 PM   #8
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Early Bird Registration ends today!
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Old 01-26-2015, 04:09 AM   #9
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UPDATE: Good news!

The ecSeq Events-Team has just decided that there will be no increase in attendance fee after 15th January 2015. All participants who already paid the increased fee, will be refunded.
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Old 07-01-2015, 12:39 AM   #10
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Upcoming workshop: A Beginner's Guide to RNA-Seq Data Analysis
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