The operation interface of miRSeq. miRSeq is composed of readPro and readMap. (a) readPro deals with raw sequence reads in fastq format by collapsing raw reads into unique reads, tabulating read count, and trimming 3′ adaptor. (b) readMap is responsible for mapping the reads back to known annotations, classifying reads into different categories, determining miRNA expression profile, reporting 3′ end modification patterns, and analyzing isomiR forms.