Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu

Most approaches to transcript quantification rely on fixed reference annotations. However, the transcriptome is dynamic, and depending on the context, such static annotations contain inactive isoforms for some genes while they are incomplete for others. To address this, we have developed Bambu, a method that performs machine-learning based transcript discovery to enable quantification specific to the context of interest using long-read RNA-Seq data. To identify novel transcripts, Bambu employs a precision-focused threshold referred to as the novel discovery rate (NDR), which replaces arbitrary per-sample thresholds with a single interpretable parameter. Bambu retains the full-length and unique read counts, enabling accurate quantification in presence of inactive isoforms. Compared to existing methods for transcript discovery, Bambu achieves greater precision without sacrificing sensitivity. We show that context-aware annotations improve abundance estimates for both novel and known transcripts. We apply Bambu to human embryonic stem cells to quantify isoforms from repetitive HERVH-LTR7 retrotransposons, demonstrating the ability to estimate transcript expression specific to the context of interest.