TEmerics: a pipeline for the identification and analysis of chimeric gene-TE transcripts

Garcia Andrés, Albert

TEmerics: a pipeline for the identification and analysis of chimeric gene-TE transcripts

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Garcia Andrés, A. TEmerics: a pipeline for the identification and analysis of chimeric gene-TE transcripts. 2024. handle: http://hdl.handle.net/10230/68915

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Abstract

Transcriptome diversification drives proteome diversity across species, with alternative splicing creating cell-type-specific protein isoforms for organism homeostasis. Transposable element (TE) insertions generate gene-TE chimeras, but identifying these transcripts is challenging due to limited scalability in existing pipelines. This work introduces TEmerics, a Snakemake pipeline for detecting and analyzing chimeric gene-TE transcripts. Benchmarking against ChimeraTE, a similar tool, was tested for performance and accuracy. Analysis of RNA-seq data from six Drosophila melanogaster strains under stress and control conditions revealed that over 10% of gene-TE chimeras appear only under stress. Future improvements for TEmerics were also identified.