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bioRxiv · 10.64898/2026.10.26.761703

Transcript quantification using context-aware MAPQ modeling

Hicks, S. C.·Parthiban, S.
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Abstract

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.

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Hicks, S. C., Parthiban, S.. 2026-10-31. Transcript quantification using context-aware MAPQ modeling. https://doi.org/10.64898/2026.10.26.761703

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