Transcript quantification using context-aware MAPQ modeling

Long-read RNA-sequencing enables accurate transcript-level quantification, but prior static filtering of MAPping Quality (MAPQ) can ignore transcriptome-intrinsic ambiguity, and discarding reads on this basis distorts abundance estimates. We present CALMeR (Context-Aware Long-read MAPQ-based Rescuer), which conditions MAPQ filtering on transcript properties rather than a fixed cutoff. CALMeR fits a zero-one inflated beta regression on various transcript and read-level features to model the expected MAPQ distribution for each alignment. Reads whose MAPQ fits this context, such as low-MAPQ reads from multi-isoform genes and paralog families are retained; reads with anomalously low MAPQ are removed as likely artifacts. Retained reads can be summed per transcript or passed to any downstream quantifier. Compared with a MAPQ ≥ 1 filter and expectation-maximization-based transcript quantification methods, CALMeR recovers more spike-in transcripts and better matches known spike-in concentrations. CALMeR is available at https://github.com/sparthib/CALMeR.