Schedule

####This course is given at Navet (E10) at BMC. 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 (Eva Molin)
09.15-10.15 Lecture: Introduction to Linux (Martin Dahlö)
10.15-12.00 Exercise: Introduction to Linux (Martin Dahlö, Jacques Dainat, Sebastian DiLorenzo, Manfred Grabherr)
12.00-13.00 Lunch
13.00-13.45 Lecture: Introduction to UPPMAX/UPPNEX (Martin Dahlö)
13.45-17.00 Exercise: Introduction to UPPMAX/UPPNEX (Martin Dahlö, Jacques Dainat, Martin Norling)

Tuesday
Room: Trippelrummet, E10, ground floor
09.00-09.20 Lecture: Introduction to File Types in Bioinformatics (Martin Dahlö)
09.20-11.00 Exercise: Introduction to File Types in Bioinformatics (Martin Dahlö, Åsa Björklund, Martin Norling, Manfred Grabherr)
11.00-12.00 Lecture: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats (Anna Johansson)
12.00-13.00 Lunch
13:00-17:00 Exercise: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part I (Anna Johansson, Jacques Dainat, Johan Reimegård)

Wednesday
Room: Trippelrummet, E10, ground floor
09:00-12:00 Exercise: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part II (Anna Johansson, Martin Dahlö, Pall Olason)
12.00-13.00 Lunch
13.00-14.30 Lecture: Next Generation Sequencing Overview (Olga Vinnere Pettersson)
14.45-15.45 Lecture: NGS and bioinformatics analysis pipelines (Adam Ameur)
16.00-17:00 Project discussion workshop - (Adam Ameur, Olga Vinnere Pettersson, Henrik Lantz, Thomas Källman)

18:00-> Course dinner at Koh Phangan

Thursday
Room: Trippelrummet, E10, ground floor
09:00-09.30 Lecture: The National Bioinformatics Infrastructure Sweden (Björn Nystedt)
09:45-10:45 Lecture: RNA sequencing, transcriptome and expression quantification (Thomas Källman)
10:45-12:00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Thomas Källman, Jacques Dainat, Manfred Grabherr)
12.00-13.00 Lunch
13:00-17:00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Thomas Källman, Martin Norling)

Friday
Room: Trippelrummet, E10, ground floor
09:00-12.00 Exercise: RNA sequencing, transcriptome and expression quantification part III (Thomas Källman, Manfred Grabherr, Pall Olason, Henrik Lantz)
12.00-13.00 Lunch
13:00-15.00 Project discussion (Thomas Källman, Henrik Lantz, Adam Ameur, Olga Vinnere Pettersson, Anna Johansson, Pall Olasson, Manfred Grabherr)