You can quantify #transposon expression in your short-read library in #locus level more accurately with LocusMasterTE and long-read count matrix from the same tissue :D

Integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression
https://www.biorxiv.org/content/10.1101/2023.03.21.533716v1

#TransposableElement #transcriptomics #RNAseq #RNA #ShortRead #LongRead #illumina #nanopore