FA COST Action TD0801 StatSeq
BMBS COST Action BM1006 SeqAhead
Sequence Data Analysis Training School |
Course Materials can be found here |
| Welcome to this training school, organised by the European Research Group EADGENE_S , and the COST Actions StatSeq (TD0801) and SeqAhead (BM1006). This page contains information and details on registration as well as application for COST travel grants. | |||||||||||||||||||||
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Dates : December 10 - 14, 2012 The course will start on Monday December 10th after lunch at 1.00 pm, and will end with lunch on Friday 14th of December. | |||||||||||||||||||||
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Aim : The course is focussed on learning to analyse sequence data by applying the state of the art methods to real datasets. Data analysis exercises will be carried out by participants in a virtual server environment. Throughout the course the aim will be to learn useful approaches and strategies for analysing your data, to learn about the important algorithms and their software implementations, and to learn how to use scripting language(s) to connect different available software tools to construct a data analysis pipeline. | |||||||||||||||||||||
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Outline : Day 1 - Introduction to using the Linux operating system for large scale data analysis. - Course dinner, followed by an invited presentation (TBA) and drinks. Day 2 - Use of Cloud computing in sequence data analysis. - Sequence data quality control and trimming of sequence data. - Quality measures and filtering of sequence data to avoid downstream problems. Day 3 - Mapping of next generation sequence reads. - SNP discovery from NGS data. Day 4 - sRNAseq (miRNA analysis) - Measuring (differential) expression levels from RNA-seq - Course dinner, followed by an invited presentation (TBA) and drinks. Day 5 - De Novo assembly Data standards (BAM etc.) will be discussed for all topics throughout the course. Exercises in a virtual server environment are an intricate part of the course. | |||||||||||||||||||||
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Instructors : - Christoph Klopp, INRA - Toulouse, France. - Mick Watson, The Roslin Institute - Edinburgh, United Kingdom. website - Hendrik-Jan Megens, Wageningen University - Wageningen, the Netherlands. | |||||||||||||||||||||
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Target audience : The course is designed for PhD students and postdoctoral fellows working with high volume next generation sequence data. Participants are expected to be familiar with sequence data and general genomics concepts. Although an introduction to working with sequence data in the Linux environment is part of the course, participants should prepare by learning the basic Linux skills if they do not already have them. The aim of the course is to teach methods, algorithms and strategies that allow participants to turn next generation sequence data into biologically relevant information such as sequence variants and expression levels. Some examples of downstream analyses that makes use of this data will be included. A combination of lectures and exercises will allow participants to get a feeling of both theory and practical application. | |||||||||||||||||||||
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Course Fee1 : | |||||||||||||||||||||
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| 1Fee include course materials, daily coffee, tea and lunch, and a course dinner. Hotel accommodation and traveling is not included. | |||||||||||||||||||||
| 2The European Research Group EADGENE_S (see www.eadgene.info ) participants qualify for the reduced rate. The list of partners in EADGENE_S can be found here . | |||||||||||||||||||||
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3Subsidy for the COST Action STATSEQ participants: The
EU COST Action StatSeq (see www.statseq.eu ) has funds for
10 travel grants of € 1000,- (max.) This grant is meant for participants who are: I. Early Stage Researcher, i.e., doing a PhD or recently completed a PhD (max. 8years ago) II. Currently working in a country that is participating in (= signed the StatSeq Action MoU) the COST Action StatSeq. The list of participating countries can be found here . | |||||||||||||||||||||
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4Subsidy for the COST Action SEQAHEAD participants: The
EU COST Action SeqAhead (see www.seqahead.eu ) has funds for
10 travel grants of € 1000,- (max.) This grant is meant for participants who are: I. Early Stage Researcher, i.e., doing a PhD or recently completed a PhD (max. 8years ago) II. Currently working in a country that is participating in (= signed the SeqAhead Action MoU) the COST Action SeqAhead. The list of participating countries can be found here . | |||||||||||||||||||||
| NB. Candidates selected for travel grants of STATSEQ or SEQAHEAD qualify for the reduced registration fee. | |||||||||||||||||||||
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Selection of candidates to be awarded the travel grant will be based on : | |||||||||||||||||||||
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| To apply for a EU-COST Action travel grant, please send information regarding the above-mentioned criteria along with your application form. The application form contains a section where the required information can be filled. This is the same form as the one found below under "Registration" and can be downloaded here . | |||||||||||||||||||||
| The application form, including the travel grant application, needs to be send to john.bastiaansen@wur.nl | |||||||||||||||||||||
| For the travel grant application please note the following dates: | |||||||||||||||||||||
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Course location : The course will be organized at the ZODIAC building of the Animal Sciences Group, on Wageningen Campus, Wageningen University, De Elst 1, 7608 WD Wageningen, the Netherlands. | |||||||||||||||||||||
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Registration : To register for the course please download the application form here and send it to john.bastiaansen@wur.nl. The top part of the form needs to be filled to apply for participation in the course. The bottom part of the form is only needed if you are applying for a COST travel grant (see section "Travel Grants" above). Full registration only occurs once you have provided us with the requested information as stated above, and after you will receive an official registration confirmation by one of the course organizers. | |||||||||||||||||||||
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Hotel Accommodation : Wageningen has several hotels to choose from: | |||||||||||||||||||||
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The first three hotels and the campus are easily accessible by
public transport (Bus
nr. 88, also called 'de Valleilijn'). These buses (blue-colored) operate within 7
minutes time-intervals and connect Wageningen center (bus terminal 'Stadsbrink')
with the main rail road station Ede-Wageningen (train going to Nijmegen/Arnhem -
via Utrecht - departing from Amsterdam or Airport Amsterdam
(Schiphol) and the
same for the way back). The listed hotel nr. 4 is easily accessible by car, but hardly by public transportation. The nearby town, Ede, has also some hotels to choose from: | |||||||||||||||||||||
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Additional information : | |||||||||||||||||||||
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