TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments

Transposable Elements (TEs) play key roles in crucial biological pathways. Therefore, several tools enabling the quantification of their expression were recently developed. However, many of the existing tools lack the capability to distinguish between the transcription of autonomously expressed TEs and TE fragments embedded in canonical coding/non-coding non-TE transcripts. Consequently, an apparent change in the expression of a given TE may simply reflect the variation in the expression of the transcripts containing TE-derived sequences.

To overcome this issue, we have developed TEspeX, a bioinformatics pipeline that quantifies the TE expression at the consensus level without taking into account reads mapping to any annotated non-TE transcript. TEspeX is a flexible tool, developed to measure the expression of any TE, regardless of its classification.