CLC workshop 23.11.2016
Contents
Introduction
The IT Services of ETH and Qiagen/CLC Bio are organizing a two-day workshop about CLC Genomics Workbench & Server.
Time and place
The workshop will take place on 23-24 November 2016 in the LEE building of ETH (room E101).
Agenda
Day 1 (Wednesday 23.11.2016)
| Begin | End | Description |
|---|---|---|
| 08:30 | 08:35 | Welcome |
| 08:35 | 09:30 | Introduction to the Workbench, plugins and connection to the server |
| 09:30 | 10:25 | Data import, data quality and trimming |
| 10:25 | 10:45 | Break |
| 10:45 | 11:40 | Toolbox and running some examples depending on the interest |
| 11:40 | 12:10 | Demonstration of Genomics Server |
| 12:10 | 13:15 | Lunch break |
| 13:15 | 14:10 | Workflows and batch processing |
| 14:10 | 15:05 | Infrastructure, how to optimize usage of the server |
| 15:05 | 15:25 | Break |
| 15:25 | 16:20 | Genome finishing / MGM |
| 16:20 | 17:00 | Questions & answers |
Day 2 (Thursday 24.11.2016)
| Begin | End | Description |
|---|---|---|
| 08:30 | 09:00 | Quick presentation of biomedical workbench / server including IVA / IPA integration |
| 09:00 | 09:40 | Walk through IVA with a look at QCI (part 1) |
| 09:40 | 10:00 | Break |
| 10:00 | 10:45 | Walk through IVA with a look at QCI (part 2) and introduction to IPA |
| 10:45 | 11:45 | Walk through IPA |
| 11:45 | 12:00 | End & farewell |
Registration
Attendance is free for members of ETH, but registration is required. Please register here.
Due to space reasons, the number of participants is limited to 60. Registrations will be granted on a first-come, first-served basis. However the organizers reserve the right to accept or deny registrations to ensure that a single group does not monopolize the workshop.
Prerequisites
Hands-on sessions require that participants bring their own laptop with CLC Genomics Workbench 9.0.1 installed. This software can be downloaded from the IT Shop of ETH.
Participants who wish to use the CLC Genomics Server on the Euler cluster should contact cluster support one week before the workshop.
Course material
You can download the sample data from the CLC Bio website:
- http://resources.qiagenbioinformatics.com/tutorials/RNASeq-droso.pdf
- http://download.clcbio.com/testdata/RNA_Seq_Droso2.zip
- http://resources.qiagenbioinformatics.com/tutorials/Resequencing-and-tracks-chrM.pdf
- http://download.clcbio.com/testdata/chrM-tutorial-data.zip
Qiagen support information
If you would like to contact the Qiagen support, then please write to the following email address:
AdvancedGenomicsSupport@qiagen.com
Your feedback about the CLC workshop
Please take a minute and provide us some feedback about CLC workshop. This will help us to learn on how to improve future workshops.
http://tinyurl.com/clc-eth-2016
Slides
Please find below the slides of the presentations that were given at the workshop. The slides from the presentations of Holger Karas will be uploaded soon.
Michal Okownieski and Samuel Fux:
Elodie Dubus (Qiagen):
