Quantitative nuclease protection assay (qNPA) method and the present disclosure provides an improved quantitative nuclease protection sequencing (qNPS) method. The disclosed method, using (NPP) nuclease protection probes containing (3-end) flanking sequence to provide amplification and / or sequence universal hybridization arrays, and / or 3 'end 5' end. The disclosed method can be used to detect or sequencing a target nucleic acid molecule, such as nucleic acid molecules present in the sample is insoluble or is fixed.
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