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training:ngstraining [2021/06/07 12:17] keime [3 RNA sequencing : library preparation and experimental design] |
training:ngstraining [2023/05/16 16:07] (current) keime [Introduction to Next Generation Sequencing data analysis] |
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| - | ====== Introduction to Next Generation Sequencing data analysis ====== | + | ====== Introduction to RNA-seq and ChIP-seq data analysis ====== |
| - | ===== 2021, June 17-18-21 ===== | + | ===== 2023, 05/31 and 06/01-02 ===== |
| ==== - Illumina Sequencing technology ==== | ==== - Illumina Sequencing technology ==== | ||
| ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ||
| - | ^ Content | {{:training:2106ngsbioinfo_1_ngs.pdf|Lecture}} | | + | ^ Content | {{:training:2305ngsbioinfo_1_ngs.pdf|Lecture}} | |
| ==== - Introduction to Galaxy ==== | ==== - Introduction to Galaxy ==== | ||
| ^ Instructor ^ [[slegras@igbmc.fr|Stephanie Le Gras]] ^ | ^ Instructor ^ [[slegras@igbmc.fr|Stephanie Le Gras]] ^ | ||
| - | ^ Content | {{:training:2009NGSbioinfo_02a_galaxy.pdf|Lecture}} | | + | ^ Content | {{:training:2305NGSbioinfo_02a_galaxy.pdf|Lecture}} | |
| - | ^ ::: | {{:training:2009ngsbioinfo_02b_galaxy_correction.pdf|Answers to practical session}} | | + | ^ ::: | {{:training:2305ngsbioinfo_02b_galaxy_correction.pdf|Answers to practical session}} | |
| + | ^ ::: | [[https://usegalaxy.fr/join-training/ngstrainingstras23|Register for TiASS]] | | ||
| + | ^ ::: | [[https://usegalaxy.fr/u/stephanie/h/ngs-data-analysis-training-strasbourg-1|Link to shared history]] | | ||
| ==== - RNA sequencing : library preparation and experimental design ==== | ==== - RNA sequencing : library preparation and experimental design ==== | ||
| ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ||
| - | ^ Content | {{:training:2106ngsbioinfo_3_rnaseq_preplib_expdesign.pdf|Lecture}} | | + | ^ Content | {{:training:2305ngsbioinfo_3_rnaseq_preplib_expdesign.pdf|Lecture}} | |
| ==== - Introduction to practical sessions ==== | ==== - Introduction to practical sessions ==== | ||
| ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ||
| - | ^ Content | {{:training:2009ngsbioinfo_4_intro_practical.pdf|Lecture}} | | + | ^ Content | {{:training:2305ngsbioinfo_4_intro_practical.pdf|Lecture}} | |
| ==== - Quality control of Illumina data ==== | ==== - Quality control of Illumina data ==== | ||
| ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ||
| - | ^ Content | {{:training:2009ngsbioinfo_5_qc.pdf|Lecture}} | | + | ^ Content | {{:training:2305ngsbioinfo_5_qc.pdf|Lecture}} | |
| ==== - NGS read mapping ==== | ==== - NGS read mapping ==== | ||
| ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ||
| - | ^ Content | {{:training:2009ngsbioinfo_6_mapping.pdf|Lecture}} | | + | ^ Content | {{:training:2305ngsbioinfo_6_mapping.pdf|Lecture}} | |
| - | ^ ::: | {{:training:2009ngsbioinfo_6_mapping_corrections.pdf|Answers to practical session}} | | + | ^ ::: | {{:training:2305ngsbioinfo_6_mapping_corrections.pdf|Answers to practical session}} | |
| ==== - Analysis of RNAseq data ==== | ==== - Analysis of RNAseq data ==== | ||
| ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ||
| - | ^ Content | {{:training:2009ngsbioinfo_7_rnaseq_analysis.pdf|Lecture}} | | + | ^ Content | {{:training:2305ngsbioinfo_7_rnaseq_analysis.pdf|Lecture}} | |
| - | ^ ::: | {{:training:2009ngsbioinfo_7_rnaseq_analysis_corrections.pdf|Answers to practical session}} | | + | ^ ::: | {{:training:2305ngsbioinfo_7_rnaseq_analysis_corrections.pdf|Answers to practical session}} | |
| ==== - Data mining with Ensembl Biomart ==== | ==== - Data mining with Ensembl Biomart ==== | ||
| ^ Instructor ^ [[slegras@igbmc.fr|Stephanie Le Gras]] ^ | ^ Instructor ^ [[slegras@igbmc.fr|Stephanie Le Gras]] ^ | ||
| - | ^ Content | {{:training:2009ngsbioinfo_08a_biomart.pdf|Lecture}} | | + | ^ Content | {{:training:2305ngsbioinfo_08a_biomart.pdf|Lecture}} | |
| - | ^ ::: | {{:training:2009ngsbioinfo_08b_biomart_correction.pdf|Answers to practical session}} | | + | ^ ::: | {{:training:2305ngsbioinfo_08b_biomart_correction.pdf|Answers to practical session}} | |
| ==== - Functional analysis of RNAseq data ==== | ==== - Functional analysis of RNAseq data ==== | ||
| ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ^ Instructor ^ [[keime@igbmc.fr|Celine Keime]] ^ | ||
| - | ^ Content | {{:training:2009ngsbioinfo_9_functional_analysis.pdf|Lecture}} | | + | ^ Content | {{:training:2305ngsbioinfo_9_functional_analysis.pdf|Lecture}} | |
| - | ^ ::: | {{:training:2009ngsbioinfo_9_functional_analysis_corrections.pdf|Answers to practical session}} | | + | ^ ::: | {{:training:2305ngsbioinfo_9_functional_analysis_corrections.pdf|Answers to practical session}} | |
| ==== - ChIP-sequencing: library preparation and experimental design ==== | ==== - ChIP-sequencing: library preparation and experimental design ==== | ||
| ^ Instructor ^ [[slegras@igbmc.fr|Stephanie Le Gras]] ^ | ^ Instructor ^ [[slegras@igbmc.fr|Stephanie Le Gras]] ^ | ||
| - | ^ Content | {{:training:2009ngsbioinfo_10_chipseq_libprep_expdesign.pdf|Lecture}} | | + | ^ Content | {{:training:2305ngsbioinfo_10_chipseq_libprep_expdesign.pdf|Lecture}} | |
| ==== - Analysis of ChIP-seq data ==== | ==== - Analysis of ChIP-seq data ==== | ||
| ^ Instructor ^ [[slegras@igbmc.fr|Stephanie Le Gras]] ^ | ^ Instructor ^ [[slegras@igbmc.fr|Stephanie Le Gras]] ^ | ||
| - | ^ Content | {{:training:2009ngsbioinfo_11a_chipseq_dataanalysis.pdf|Lecture}} | | + | ^ Content | {{:training:2305ngsbioinfo_11a_chipseq_dataanalysis.pdf|Lecture}} | |
| - | ^ ::: | {{:training:2009NGSbioinfo_11b_chipseq_dataanalysis_correction.pdf|Answers to practical session}} | | + | ^ ::: | {{:training:2305NGSbioinfo_11b_chipseq_dataanalysis_correction.pdf|Answers to practical session}} | |
| ==== - NGS analysis automatization: Galaxy workflows ==== | ==== - NGS analysis automatization: Galaxy workflows ==== | ||
| ^ Instructor ^ [[slegras@igbmc.fr|Stephanie Le Gras]] ^ | ^ Instructor ^ [[slegras@igbmc.fr|Stephanie Le Gras]] ^ | ||
| - | ^ Content | {{:training:2009ngsbioinfo_12_workflows.pdf|Lecture}} | | + | ^ Content | {{:training:2305ngsbioinfo_12_workflows.pdf|Lecture}} | |
| ==== - Correlation of RNA-seq and ChIP-seq data ==== | ==== - Correlation of RNA-seq and ChIP-seq data ==== | ||
| ^ Instructor ^ [[slegras@igbmc.fr|Stephanie Le Gras]] ^ | ^ Instructor ^ [[slegras@igbmc.fr|Stephanie Le Gras]] ^ | ||
| - | ^ Content | {{:training:2009ngsbioinfo_13a_chipseq_rnaseq_correlation.pdf|Lecture}} | | + | ^ Content | {{:training:2305ngsbioinfo_13a_chipseq_rnaseq_correlation.pdf|Lecture}} | |
| - | ^ ::: | {{:training:2009ngsbioinfo_13b_chipseq_rnaseq_correlation_correction.pdf|Answers to practical session}} | | + | ^ ::: | {{:training:2305ngsbioinfo_13b_chipseq_rnaseq_correlation_correction.pdf|Answers to practical session}} | |
