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This course is given at the University of Gothenburg. The lecture slides and lab instructions will be uploaded when the material is finalized by the responsible teacher.
Room: Folke Andreasson, Medicinareg. 11
12.30-14.00 [Lecture: Next Generation Sequencing Overview](slides/Sequencing_OVP 2014_d.pptx) (Olga Vinnere Pettersson)
14.00-15.00 Lecture: NGS and bioinformatics analysis pipelines (Adam Ameur)
15.30-17:00 Project discussion - (Adam Ameur, Olga Vinnere Pettersson)
Room: Ingegerd Eriksson Medicinareg. 1, Academicum
09.00-09.10 [Lecture: Introduction to SciLifeLab](slides/150518_SciLifeLab_presentation_NGS data_Gbg.pptx) (Eva Molin)
09.10-10.00 Lecture: Introduction to Linux (Martin Dahlö)
10.00-12.00 Exercise: Introduction to Linux (Martin Dahlö, Marcela Dávila, Mats Töpel, Magnus Alm Rosenblad)
12.00-13.00 Lunch
13.00-14.00 Lecture: Introduction to UPPMAX/UPPNEX (Martin Dahlö)
14.00-16.00 Exercise: Introduction to UPPMAX/UPPNEX (Martin Dahlö, Marcela Dávila, Mats Töpel, Magnus Alm Rosenblad)
16.00-16.20 Lecture: Introduction to File Types in Bioiformatics (Martin Dahlö)
16.20-17.15 Exercise: Introduction to File Types in Bioinformatics (Martin Dahlö, Marcela Dávila, Mats Töpel, Magnus Alm Rosenblad)
Room: Ingegerd Eriksson Medicinareg. 1, Academicum
09.00-10.00 Lecture: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats (Anna Johansson)
10:15-12:00 Exercise: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part I (Anna Johansson, Katarina Truvé, Agata Smialowska, Mats Töpel, Magnus Alm Rosenblad)
12.00-13.00 Lunch
Room: Birgit Thilander Medicinareg. 1, Academicum
13:00-17:00 Exercise: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part II (Anna Johansson, Katarina Truvé, Agata Smialowska, Mats Töpel, Magnus Alm Rosenblad)
Room: Folke Andreasson Medicinareg. 11
09:00-11:30 Exercise: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part III (Anna Johansson, Katarina Truvé, Agata Smialowska, Mats Töpel)
11:30-12.00 Lecture: The Wallenberg Advanced Bioinformatics Initiative (WABI) and the Bioinformatics Infrastructure for Life Sciences (BILS) (Anna Johansson)
12.00-13.00 Lunch
13:00-14:00 Lecture: RNA sequencing, transcriptome and expression quantification (Thomas Källman)
Room: Ingegerd Eriksson Medicinareg. 1, Academicum
14:15-17:00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Thomas Källman, Katarina Truvé, Agata Smialowska, Mats Töpel)
18:00-20:00 Dinner at Incontro
Room: Ingegerd Eriksson Medicinareg. 1, Academicum
09:00-12.00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Thomas Källman, Katarina Truvé, Agata Smialowska, Mats Töpel)
12.00-13.00 Lunch
13:00-15.00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Thomas Källman, Katarina Truvé, Agata Smialowska, Mats Töpel)