NGS - Quality control, Alignment, Visualisation - February 2019
Section outline
-
NGS - Quality control, Alignment, Visualisation
27 February - 01 March 2019
room 331 / 3. OG West, Universität Bern, Hochschulstrasse 4 (main building of the University of Bern).
This page is addressed to registered participants. To access course description and application form, please click here.
This course will be taught by Walid Gharib, for any assistance, please contact training@sib.swiss.
-
Wednesday 27 February
Introduction to technologies and applications, NCBI E-Utilities and sequencing data retrieval
9:15 - 10:30 - Introduction to technologies and applications (1)
- Ion Torrent Sequencing - Semiconductor sequencing
- llumina - sequencing by synthesis
10:30 - 11:00 - Coffee Break
11:30 - 12:15 - Introduction to technologies and applications (2)
- Pacific Biosciences - SMRT Sequencing
- Oxford Nanopores - MinIon, GridIon
12:15 - 13:30 - Lunch Break
13:30 - 13:45 - NCBI: E-utilities using Unix command line
13:45 - 15:00 - E-utilities usage - Practicals15:00 - 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)Thursday 28 February
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 reads10:30 - 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
15h30 - 17:00 - Sorting, Indexing the alignment and quick visualization using IGV genome viewerFriday 29 February
9:00 - 10:30: Visualisation using IGV lecture
10:30 - 11:00: Coffee break11:00 - 12:15: Practicals using cancer variants dataset
12:15 - 13:30: Lunch Break
13:30 - 15:30: Practicals using RNAseq and CHIPseq datasets
15h30 - 17:00: useful tips and tricks in NGS/concluding remarks
END
- Ion Torrent Sequencing - Semiconductor sequencing
-
Participants should install "The Integrative Genome Viewer (IGV)" on their respective machines.
Basic understanding of working with command line tools on Linux or Windows-based operating systems is required. If you do not feel comfortable with UNIX commands, please take our UNIX fundamentals e-learning module.