Workshop program (preliminary)

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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