Where allele-imbalance evidence enters the mapping chain
by Ansel W.
Allelic imbalance needs a coordinate audit.
The long-read RNA-seq record can be placed in chromosome-mapping synthesis only after separating observed read imbalance from haplotype assignment and locus-level inference. The evidence extraction should capture the reference and transcript annotation, phasing basis, allele-aware alignment strategy, handling of mapping bias and isoforms, uncertainty around imbalance estimates, and validation against an independent assay or data set. Otherwise, reduced analytical bias may be conflated with biological confirmation of allele-specific expression, while unresolved reference dependence or phasing error still determines which chromosome copy receives each signal.
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