MAJEC: unified gene, isoform, and locus-level transposable element quantification from RNA-seq: Supplementary Data and Analysis Notebooks

Supplementary data for: MAJEC: Momentum-Accelerated Junction-Enhanced Counting for RNA-seq transcript quantification Four datasets used to benchmark MAJEC against Salmon, RSEM, TEtranscripts, and Telescope ### long_bench.tar.gz (667 MB → ~1.1 GB uncompressed) **8 lung cancer cell lines** — paired-end Illumina short-read quantification benchmarked against PacBio, ONT, and direct-RNA long-read ground truth. ### sequins.tar.gz (111 MB → ~125 MB uncompressed) **Sequins v2.4 synthetic spike-ins** — 160 synthetic RNA isoforms with known concentrations (Mix A/B), from Dong et al. 2021 (PMID 33937765). ### tcell_SRA.tar.gz (145 MB → ~312 MB uncompressed) **T-cell activation time course** — 3 timepoints with PacBio long-read ground truth (IsoQuant). ### te_benchmark.tar.gz (483 MB → ~900 MB uncompressed) **TE locus-level quantification** — CD81KO decitabine vs DMSO (6 samples, 150 bp PE, reverse-stranded). Benchmarks MAJEC against TEtranscripts and Telescope for transposable element quantification.