Files for Main Figures

Fig 1 Long_read_TE_fc: Transposable elements individual quantified featureCounts result using long-read Short_read_TE_fc: Transposable elements individual quantified featureCounts result using short-read Long_read_coding_genes_fc: Coding genes quantified featureCounts result using long-read Short_read_coding_genes_fc: Coding genes individual quantified featureCounts result using long-read Inhouse_HCT116_telescope.tsv: Telescope output using inhouse HCT116 with random option LocusMasterTE-TE_counts.tsv: LocusMasterTE output using inhouse HCT116 telescope-TE_counts: Telescope output using inhouse HCT116 Fig 3 Simulated_reads_quantification_mat : Quantified TEs in TPM counts in simulated short-read measured by 7 approaches. File used for main figure 3. Fig 4 6 Cell lines TE matrices quantified by long-read, Telescope (short-read), LocusMasterTE (short-read) SG-Nex_A549: TE counts by long-read, Telescope (short-read), LocusMasterTE (short-read) using A549 cell line in SG-NEx study SG-Nex_HepG2: TE counts by long-read, Telescope (short-read), LocusMasterTE (short-read) using HepG2 cell line in SG-NEx study SG-Nex_HCT116: TE counts by long-read, Telescope (short-read), LocusMasterTE (short-read) using HCT116 cell line in SG-NEx study SG-Nex_K562: TE counts by long-read, Telescope (short-read), LocusMasterTE (short-read) using K562 cell line in SG-NEx study SG-Nex_MCF-7: TE counts by long-read, Telescope (short-read), LocusMasterTE (short-read) using MCF-7 cell line in SG-NEx study Inhouse_HCT116: TE counts by long-read, Telescope (short-read), LocusMasterTE (short-read) using HCT116 sample generated by our lab Fig 5 mutational_profile_TCGA-COAD: Mutational profiling of TCGA-COAD patients with MDA5-protected Alu elements from 5-azacytidine-treated ADAR wild-type samples.