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Schedule |
Click the heading of a topic to see the lecture slides or lab instructions. Slides are added as the course progresses.
Monday
Room: Trippelrummet, E10, ground floor
09.00-09.15 Registration and Welcome, presentation of SciLifeLab (Eva Molin)
09.15-10.00 Lecture: Introduction to Linux (Martin Dahlö)
10.00-12.00 Exercise: Introduction to Linux (Martin Dahlö, Alvaro Martinez Barrio, Anders Larsson, Frederic Haziza)
12.00-13.00 Lunch at BMC restaurant
13.00-14.00 Lecture: Introduction to UPPMAX/UPPNEX (Martin Dahlö)
14.00-17.00 Exercise: Introduction to UPPMAX/UPPNEX (Martin Dahlö, Alvaro Martinez Barrio, Anders Larsson, Frederic Haziza)
Tuesday
Room: Trippelrummet, E10, ground floor
09.00-09.30 Lecture: File types in bioinformatics (Martin Dahlö)
09.30-12.00 Exercise: File types in bioinformatics (Martin Dahlö, Pall Olason, Johan Viklund, Per Unneberg)
12.00-13.00 Lunch at BMC restaurant
13:00-14:00 Lecture: Advanced Linux usage (Martin Dahlö)
14:00-17:00 Exercise: Advanced Linux usage (Martin Dahlö, Pall Olason, Johan Viklund, Per Unneberg)
Wednesday
Room: Trippelrummet, E10, ground floor
09.00-11.00 Lecture: Next Generation Sequencing Overview (Olga Vinnere Pettersson)
11:00-12.00 Lecture: NGS and bioinformatics analysis pipelines (Adam Ameur)
12.00-13.00 Lunch at BMC restaurant
13.00-14.00 Lecture: Alignment with BWA; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats (Anna Johansson)
14.00-17.00 Exercise: Alignment with BWA; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part I (Anna Johansson, Johan Reimegård, Sebastian DiLorenzo, Lucile Soler)
18:00- Course dinner at TBA
Thursday
Room: Trippelrummet, E10, ground floor
09:00-12.00 Exercise: Alignment with BWA; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part II (Anna Johansson, Sebastian DiLorenzo, Johan Reimegård, Lucile Soler)
12.00-13.00 Lunch at BMC restaurant
13.00-14:00 Lecture: RNA sequencing, transcriptome and expression quantification (Thomas Källman)
14.00-17:00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Thomas Källman, Agata Smialowska, Olga Dethlefsen, Åsa Björklund)
Friday
Room: Trippelrummet, E10, ground floor
09:00-12:00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Thomas Källman, Agata Smialowska, Olga Dethlefsen, Åsa Björklund)
12.00-13.00 Lunch at BMC restaurant
13:00-15.00 Data management and open discussions (Niclas Jareborg, Olga Vinnere Pettersson, Adam Ameur, Agata Smialowska, Olga Dethlefsen, Henrik Lantz)