T3E: TRANSPOSABLE ELEMENT ENRICHMENT ESTIMATOR

Because of their repetitive nature, short sequencing reads derived from transposable elements (TEs) cannot be unambiguously mapped to the reference genome. As a result, most genomic analyses neglect over 50% of the human genome. Here, we present T3E, an algorithm to characterize the histone modifications associated with TEs from Chromatin Immunoprecipitation Sequencing (ChIP-seq) data. T3E relies on the structure of the ChIP seq control experiment to assess enrichment. When applying T3E to five ChIP-seq libraries we found consistently fewer enrichments compared to a strategy that assumes a random distribution of the reads across the genome, suggesting that the latter has a high false positive rate. This provides a framework for the functional analysis of TEs.