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May 25, 14:00 – 17:00 h: RepeatExplorer: principles and applications [ZOOM]
- Invitation to the workshop & instructions (J. Macas)
- Principles and applications of RepeatExplorer (J. Macas)
- RepeatExplorer pipeline and associated tools (P. Novak)
- break
- REXdb database and DANTE (P. Neumann)
- Using RE output for repeat annotation and quantification (J. Macas)
- Practical training I – assignment of tasks (P. Novak)
May 26 – May 31: Practical training part I [conducted individually, based on the provided data and videotutorials]
- Galaxy environment and RepeatExplorer server
- Protocol 1: Repeat analysis in a single species
- quality control and preprocessing of Illumina reads
- setting up the RepeatExplorer run
- download and exploration of resulting files
- Protocol 2: Comparative repeat analysis in multiple species
- read preprocessing, employing Galaxy tools for parallel processing
- setting up the RepeatExplorer run
- exploration of resulting files
- tools specific for comparative analysis
May 28, 14:00-16:00 h: Troubleshooting and discussion related to practical training I [ZOOM]
- based on the questions posted to Slack or presented during the session
June 1, 14:00 – 17:00 h: Short presentations of the workshop participants (20 + 5 min each)
- TBA
- …
June 2 – June 7: Practical training part II [conducted individually, based on the provided data and videotutorials]
- Protocol 1: evaluation and interpretation of the results
- Protocol 2: evaluation and interpretation of the results, downstream analysis
- Protocol 3: TAREAN analysis of satDNA and FISH probe design
June 5, 14:00-16:00 h: Troubleshooting and discussion related to practical training II [ZOOM]
- based on the questions posted to Slack or presented during the session
June 8, 14:00 – 17:00 h: Short presentations of the workshop participants (20 + 5 min each)
- TBA
- …
June 9 – June 10: Practical training part III [conducted individually, based on the provided data and videotutorials]
- Protocol 4: Identification of centromeric repeats using ChIP-seq analysis
- DANTE and JBrowse
June 11, 14:00-16:00 h: Troubleshooting and discussion related to practical training III [ZOOM]
- based on the questions posted to Slack or presented during the session
Register to the workshop