Course 2013

Kyoto Course on Bioinformatics for Next Generation Sequencing with Applications in Human Genetics – January 15 – 18, 2013

Day 1 EXOME AND WHOLE GENOME SEQUENCING USING MASSIVELY-PARALLEL SEQUENCERS

10:00 – 10:15 Opening remarks F. Matsuda
10:15 – 11:00 Lecture Introduction to next generation sequencing technologies and applications M. Lathrop
11:00 – 11:30 Coffee Break
11:30 – 12:30 Lecture Understanding the high-throughput sequencing data analysis workflow G. Bourque
12:30 – 13:30 Lunch
13:30 – 14:30 Lecture Quality assessment and filtering, mapping strategies for sequence reads G. Bourque
14:30 – 15:00 Coffee Break
15:00 – 16:30 Lecture and Practical Rare variants association analyses D. Weeks
16:30 – 17:30 Practical Basic Linux Staff

Day 2 APPLICATIONS TO RNA ANALYSIS AND DATA SUBMISSION

9:00 – 10:00 Lecture Introduction to RNA-seq: expression estimation and normalisation M. Gonzalez-Porta
10:00 – 11:00 Lecture Differential expression and differential exon usage M. Gonzalez-Porta
11:00 – 11:15 Coffee Break
11:15 – 12:30 Practical Dealing with raw RNA-seq data: quality assessment, filtering and mapping M. Gonzalez-Porta
12:30 – 13:30 Lunch
13:30 – 14:00 Lecture ENA introduction R. Radhakrishnan
14:00 – 14:30 Lecture SRA introduction R. Radhakrishnan
14:30 – 15:30 Lecture SRA submission, browsing, and data retrieval R. Radhakrishnan
15:30 – 16:00 Coffee Break
16:00 – 16:25 Lecture Data compression R. Radhakrishnan
16:25 – 17:55 Practical ENA submission R. Radhakrishnan

Day 3 PRACTICALS FOR EXOME AND RNA-SEQ

9:00 – 12:30 Practical Exome sequencing data analysis (~10:30 Coffee Break) G. Bourque
12:30 – 13:30 Lunch
13:30 – 17:00 Practical Dealing with aligned data (including differential expression analysis) (~15:00 Coffee Break) M. Gonzalez-Porta

Day 4 HUMAN GENETICS

9:00 – 10:00 Lecture Introduction to disease gene mapping J. Ott
10:00 – 11:00 Practical Disease gene mapping J. Ott
11:00 – 11:30 Coffee Break
11:30 – 12:30 Lecture Imputation and testing imputed SNPs M. Devoto
12:30 – 13:30 Lunch
13:30 – 14:30 Practical Imputation and testing imputed SNPs M. Devoto
14:30 – 15:30 Lecture Statistical tests for NGS data and heterogeneity statistics for association analysis D. Gordon
15:30 – 16:00 Coffee Break
16:00 – 17:00 Practical Statistical tests for NGS data and heterogeneitystatistics for association analysis D. Gordon
17:00 – 17:30 Lecture Cancer genetics and genomics: Of Mice and Men M. M. Taketo