Data analysis pipelines of high-throughput sequencing. Three different analysis approaches were applied to small RNA profiling in samples from follicular thyroid tumors. Results were obtained from mapping reads to the human genome (hg19) – closest family member sequencing (Pipeline A), mapping independent isoform sequencing (Pipeline B) and seed analysis (Pipeline C). The closest family member sequencing workflow (Pipeline A) uses bowtie2 mapping to the human genome obtained from the public repository. The isoform sequencing pipeline returns the frequency of each individual sequence isoform. Seed analysis merges counts of individual isoforms with the same miRNA seed sequence and therefore targets biological importance of miRNA isoform families (sequences) which could potentially act in concert as regulators of thyroid cells.