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