Example outputs from CPAP-miRSeq (MCF7 dataset). A. Summary statistics of each miRNA-seq library processed. B. Raw mature miRNA expression table, weighted count for miRNAs coded by multiple pre-miRNAs. C. Normalized mature miRNA expression table by number of reads per million (RPM). D. Summarized mature miRNA expression table for those with multiple pre-cursors. These miRNAs are indistinguishable by sequence but have the same biological effect. This table is used for final differential expression analysis. E. Merged novel miRNA expression across samples. F. Integrative Genome Viewer (IGV) to visualize sequence level data for a single nucleotide variant. G. Mapped read distribution in different parts of the hairpin structure of miRNA precursor which provides a strong evidence of an authentic miRNA.