|Date||9 - 10 January 2018|
|Speaker(s)||Walid Gharib, Geoffrey Fucile|
|Cancellation deadline||2 Jan 2018|
Please note that this course is oversubscribed. We are not accepting applications, not even for the waiting list anymore.
Usage of NGS is increasing in several biological fields due to a very rapid decrease in cost. However, it often results in hundreds of Gbs of data making the downstream analysis very challenging and requires bioinformatics skills.
In this module, we will introduce the most used sequencing technologies and explain their decryption concepts.
We will also introduce the repositories e.g. the European Nucleotide Archive (ENA), Sequence Read Archive (SRA) from which you could retrieve raw data based on specific experiments. We will practice the usage of command line tools to search and fetch NGS raw data in a powerful way.
Finally, using different datasets, we will practice screening for quality control, filtering reads for better downstream analysis, mapping reads to reference genome and visualize the output.
This course is intended for life scientists who are already dealing with NGS data or willing to efficiently use publicly available NGS data, and would like to be able to start analysing them.
At the end of the course participants should be able to:
Knowledge / competencies:
Participants should have a basic understanding of working with command line tools on Linux or Windows-based operating systems. If you do not feel comfortable with UNIX commands, please take our UNIX fundamentals e-learning module.
Participants should bring their own computers and chargers. Computers should have at least 4 GB RAM, 50 GB free disk space, and WIFI preinstalled.
Participants should install "The Integrative Genome Viewer (IGV)" on their respective machines.
Please note that this course is already oversubscribed.
The registration fees for academics are 100 CHF. Participants from non-academic institutions should contact us before application.
Deadline for registration and free-of-charge cancellation is set to January 2. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to this and other general conditions, available here.
You will be informed by email of your registration confirmation.
room 331 / 3. OG West, Universität Bern, Hochschulstrasse 4 (main building of the University of Bern).
Tuesday 09 January
Introduction to technologies and applications, NCBI E-Utilities and sequencing data retrieval
9:15 - 10:30 - Introduction to technologies and applications (1)
10:30 - 11:00 - Coffee Break
11:30 - 12:15 - Introduction to technologies and applications (2)
12:15 - 13:30 - Lunch Break
13:30 - 13:45 - NCBI: E-utilities using Unix command line
13:45 - 15:00 - E-utilities usage - Practicals
15:00 - 15:30 - Coffee break
15:30 - 15:45 - Sequencing archives, SRA, ENA and DDBJ
15h45 - 17:00 - Fetching sequencing data - Practicals (Combining E-utilities and SRA tools)
Wednesday 10 January
File Formats, quality assessment, cutting/trimming/filtering and sequence alignement
9:00 - 10:00: File formats and Quality controls
9:45 - 10:30: Interpretation of a Fastqc report and acting upon for cutting/trimming reads
10:30 - 11:00: Coffee break
11:00 - 12:15: Quality control - Practicals
- Trimming/filtering quality control - Practicals
12:15 - 13:30 - Lunch Break
13:30 - 15:30 - Alignment to a reference genome - Small intro and practicals
16:00 - 17:00 - Sorting, Indexing the alignment and quick visualization using IGV genome viewer
The course will be taught by Walid Gharib.
Coordination: Patricia Palagi, Training group at SIB
We will recommend 0.5 ECTS credits for this course (given a passed exam (optional) at the end of the session).
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