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RNA-Seq workshop at Dept of Informatics, UiO

Wednesday 14th Dec, 2016

Materials can be found here:

https://etherpad.net/p/ELIXIR_Oslo_December

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RNA-Seq workshop at Dept of Informatics, UiO

Wednesday 5th Oct, 2016

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RNA-Seq workshop at Dept of Informatics, UiO

Wednesday 1st June, 2016

Elixir presentation

NeLS presentation

RNA-Seq background

RNA-Seq hands-on

NeLS file handling (please see "Handling data and storage in NeLS" document below).

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RNA-Seq workshop at Dept of Informatics, UiO

Wednesday 20th April, 2016

Elixir presentation (Ståle Nygård, OUS-Radium/UiO) 

NeLS presentation (David Fredman, CBU, UiB)

RNA-Seq background (Ståle Nygård, OUS-Radium/UiO) 

Please also see relevant material from previous workshops below, e.g the RNA-seq hands-on by Kjell Petersen.

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Workshop for NSC/NGC/NCGC at Dept of Informatics, UiO Wednesday 18th March, 2015
10:00 - 10:15  :  Welcome & introduction to Elixir (Eivind Hovig, OUS-HF - Radium/UiO) 
10:15 - 10:30  :  Overview of Elixir.no infrastructure and resources (Kjell Petersen, UiB)
10:30 - 11:00  :  Sensitive data (Gard O. Thomassen, USIT)
11:00 - 12:00  :  Tjenester for Sensitive Data (TSD) - Architecture and services (Gard O. Thomassen, USIT)

12:00 - 13:00  :  Lunch

13:00 - 14:10  :  TSD - Login [Hands-on] (Abdulrahman Azab, UiO)
14:10 - 14:50  :  TSD - Data transfer [Hands-on] (Abdulrahman Azab, UiO)

14:50 - 15:00  :  Coffee break

15:00 - 16:00  :  TSD - Running software on the command line [Hands-on] (Abdulrahman Azab, UiO)
16:00 - 17:00  :  NCGC somatic variant calling pipeline [Presentation & demo] (Daniel Vodak / Sigve Nakken, OUS-HF - Radium)

19:00 :  Dinner
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Thursday 19th March, 2015
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09:00 - 09:30  :  Introduction to Galaxy (Sveinung Gundersen / Geir Kjetil Sandve, UiO)
09:30 - 09:45  :  NSC germline variant calling pipeline (Ying Sheng)
09:45 - 10:45  :  Galaxy in TSD [Hands-on] with running of germline pipeline [Demo] (Abdulrahman Azab, UiO / Ghislain Fornous, OUS-HF - Radium)

10:45 - 11:00  :  Coffee Break

11:00 - 11:20  : Overview of National e-Infrastructure for Life Science (NeLS) (Kidane Tekle, UiB)
11:20 - 12:00  : Handling data and storage in NeLS [Hands-on] (Sveinung Gundersen, UiO)

12:00 - 13:00  :  Lunch

13:00 - 13:50  :  RNA-seq pipelines in NeLS [Hands-on] (Kjell Petersen, UiB)
13:50 - 14:20  :  MetaPipe - metagenomics pipeline in NeLS [Demo] (Alexander Raknes, UiT)

14:20 - 14:30  :  Coffee Break

14:30 - 15:00  :  Statistical genomics with the HyperBrowser [Demo] (Sveinung Gundersen, UiO)
15:00 - 16:00  :  Discussion / feedback session (Eivind Hovig, OUS-HF - Radium/UiO)
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Workshop for NCGC at the OUH-Radiumhospitalet
Monday 23rd March
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10:00 - 10:15  :  Welcome & introduction (Eivind Hovig)
10:15 - 10:45  :  Sequencing lab workflow (Leonardo Meza-Zepeda)
10:45 - 11:00  :  General data flow (Ghislain Fournous/Daniel vodák)
11:00 - 11:30  :  Tjenester for Sensitive Data (TSD) - Overview and usage (Abdulrahman Azab)
11:30 - 12:15  :  TSD [Hands-on] (Abdulrahman Azab]

12:15 - 13:00  :  Lunch

13:00 - 14:00  :  NCGC pipeline/ICGC/Annotation pipeline (Daniel Vodák, Ghislain Fournous, Sigve Nakken)
14:00 - 14:30  :  Bash, Ruby pipeline (Ghislain Fournous, Daniel Vodák)
14:30 - 14:40  :  Coffee break
14:40 - 15:30  :  NCGC pipeline [Hands-on] (Daniel Vodák, Ghislain Fournous, Sigve Nakken)
15:30 - 16:30  :  Downstream analysis options [Discussion] (Everybody, Sigve Nakken, Eivind Hovig)