IRescue: uncertainty-aware quantification of transposable elements expression at single cell level
Estimating RE expression in scRNA-seq poses significant computational challenges due to multi-mapping reads aligning to interspersed repeats. To address this limitation, we developed IRescue. IRescue adapts a gold-standard UMI-deduplication strategy to correct sequencing errors and remove PCR duplicates along with an Expectation-Maximization algorithm to probabilistically redistribute multi-mapping reads, enhancing the accuracy of RE expression estimates.