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The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created  epiTEome , a program that detects both new transposable element insertion sites and their methylation states from a single MethylC-seq dataset.  EpiTEome  outperforms other split-read insertion site detection programs, even while functioning on bisulfite-converted reads.  EpiTEome  characterizes the previously discarded fraction of DNA methylation at sites of new insertions, enabling future investigation into the epigenetic regulation of non-reference and transposed elements.

EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels