Kyoto Course on Bioinformatics for Next Generation Sequencing with Applications in Human Genetics – January 15 – 18, 2013
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Day 1 EXOME AND WHOLE GENOME SEQUENCING USING MASSIVELY-PARALLEL SEQUENCERS |
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| 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 |
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Day 2 APPLICATIONS TO RNA ANALYSIS AND DATA SUBMISSION |
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| 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 |
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Day 3 PRACTICALS FOR EXOME AND RNA-SEQ |
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| 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 |
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Day 4 HUMAN GENETICS |
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| 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 |