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Transposon Detection in C. elegans

Scripts for simulation and detection of Transposons

Simulations

Simulate transposon insertions and exsisions with BAMSurgeon and RSVSim and evaluate results

bash run_simulations.sh
bash analyze_simulations.sh

Set Up Directory Structure

mkdir data
mkdir results
mkdir piRNA
mkdir tables

Run Transposon Detection Programs

Run TEMP to detect insertion events relative to the reference and TE-Locate to detect absences or maintenance of transposons relative to the reference. In data directory:

bash run_TransposonCaller.sh

Process Transposon Caller Outputs

  • Filter out redundant calls
  • Apply read support and population frequency filters
  • Convert transposon names
  • Collapse transposons
  • Produce consistently formatted output files
bash run_ProcessTransposonCallerOutput.sh

Define Traits and Classify

  • Check for and resolve contradictory calls
  • Merge transposons
  • Generate matrix of calls
  • Filter monomorphic sites
  • Account for sites with no coverage
  • Calculate trait metrics
  • Check transposon classification and prevalence
  • Find intersection with genes
bash CleanTransposons.sh

GWAS Results

Obtain mapping results file and analyze GWAS results in context of genes of interest and piRNAs

bash PostMappings.sh