Fig. 1

The chimeric TE-mRNA concept and TIDAL implementation using RNAseq data as input. A Diagrams considering how read coverage would reflect canonical exon splicing versus a TE-gene chimera versus intron retention during transcription of the intronic TE. Split reads representing these de novo TE insertions would not be mapped to a reference genome and transcriptome, requiring a specialized bioinformatics program like TIDAL and others. B-E Diagrams of TIDAL implemented on RNAseq to detect TEs in (B), Alternative splicing isoforms (C), small deletions like InDels (D), and potential gene-fusions that are more likely artifacts of similarity in sequences between different genes because some genes are loaded into TIDAL as an IGE (immobile gene element) (E). Depicted are split reads being aligned to the genomic structural variant by scripts within TIDAL. F A common artifact of a simple T-repeat sequence from reverse-transcribing from the Poly-A during Alternative Poly-Adenylation (APA) of a Drosophila gene like GlyP, where this simple T-repeat is part of the hopper/M4DM TE sequence. This additional simple-polynucleotide filter was added to TIDAL runs on RNAseq data