Schedule

This course is given in Trippelrummet at Navet ( E10) at BMC, ground floor.

Click the heading of a topic to see the lecture slides or lab instructions

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Monday 9th
09.00-09.15 Registration and Welcome (Eva Molin)
09.15-10.30 Lecture: Introduction to Unix and UPPMAX/UPPNEX part I (Martin Dahlö)
11.00-12.00 Exercise: Introduction to Unix and UPPMAX/UPPNEX part I (Martin Dahlö, Jacques Dainat, Alvaro Martinez Barrio, Manfred Grabherr)
12.00-13.00 Lunch
13.00-13.45 Lecture: Introduction to Unix and UPPMAX/UPPNEX part II (Martin Dahlö)
13.45-17.00 Exercise: Introduction to Unix and UPPMAX/UPPNEX part II (Martin Dahlö, Sebastian DiLorenzo, Alvaro Martinez Barrio, Martin Norling)

Tuesday 10th
09.00-09.20 Lecture: Introduction to Unix and UPPMAX/UPPNEX part III (Martin Dahlö)
09.20-10.15 Exercise: Introduction to Unix and UPPMAX/UPPNEX part III (Martin Dahlö, Sebastian DiLorenzo, Martin Norling, Alvaro Martinez Barrio)
10.30-12.00 Lecture: Next Generation Sequencing Overview (Olga Vinnere Pettersson)
12.00-13.00 Lunch
13.00-14.00 Lecture: NGS and bioinformatics analysis pipelines (Adam Ameur)
14.30-17:00 Project discussion - (Adam Ameur, Olga Vinnere Pettersson, Henrik Lantz, Thomas Källman)

Wednesday 11th
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, Sebastian DiLorenzo, Jacques Dainat, Åsa Björklund)
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 II (Anna Johansson, Martin Dahlö, Jacques Dainat, Åsa Björklund)

Thursday 12th
09:00-12:00 Exercise: Alignment with BWA; Samtools; Data Processing with Picard; Variant Calling with GATK; SAM/BAM and VCF Formats part III (Anna Johansson, Martin Dahlö, Johan Reimegård, Manfred Grabherr)
12.00-13.00 Lunch
13:00-14:00 Lecture: RNA sequencing, transcriptome and expression quantification (Thomas Källman)
14:15-17:00 Exercise: RNA sequencing, transcriptome and expression quantification part I (Thomas Källman, Jacques Dainat, Johan Reimegård, Martin Norling)

Friday 13th
09:00-11.00 Exercise: RNA sequencing, transcriptome and expression quantification part II (Thomas Källman, Manfred Grabherr, Martin Norling, Pall Olason, Henrik Lantz)
11:30-12.00 Lecture: The Wallenberg Advanced Bioinformatics Initiative (WABI) and the Bioinformatics Infrastructure for Life Sciences (BILS) (Björn Nystedt)
12.00-13.00 Lunch
13:00-15.00 Exercise: RNA sequencing, transcriptome and expression quantification part III (Thomas Källman, Martin Norling, Henrik Lantz, Pall Olason)

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Topic revision: r23 - 2015-02-13 - MartinDahlo
 
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