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VRE Epigenetics

VRE Epigenetics

URGI in-house project to set up a Virtual Research Environment to study Transposable Elements and their impact on the epigenomes.


The goal is to build a research environment using:

  1. Analysis tools
  2. Visualization tools
  3. Data sharing tools
  4. Virtual Machines

Analysis tools:

  • Repeat analysis: REPET , TEiso
  • Read mapping: BWA
  • NGS Galaxy tools
  • RNASeq and ChiPseq analysis 

Visualization tools:

  • Genomes (genes, TE, RNAseq, etc.): IGV
  • TE consensus: IGV, Jalview 

Data sharing tools:

  • Files sharing: Fuse, FTP/SSH, iRODS
  • Files indexation: ElasticSearch
  • Databases: InterMine ( RepetDB ), TripleStore

Virtual Machines:

  • These tools will be installed on the Galaxy environment in Virtual Machines.
  • VMs allow easy copy and distribution.
Update: 17 Feb 2017
Creation date: 13 Feb 2017