Fig. 1

A bioinformatics pipeline for the quantification of read specifically mapping on TE. a and b Workflow and schema of the pipeline. Reads are mapped, allowing multimapping, against the reference transcriptome (composed by annotated coding and non-coding transcripts [blue] and TE consensus sequences [red]). Best scoring alignments are selected and then, to avoid selection of TE-non-specific reads, reads mapping with best scoring alignments both on transposome and transcriptome are discarded. STAR is the program used for the mapping. c Global TE expression levels calculated for every cell type using our pipeline (custom) and SalmonTE. d Quantification of TE-non-specific reads used to assess whether the increased TE expression in AB descendant cells of the 16-cell stage, evidenced by SalmonTE, is given by TE-non-specific reads quantification