Small RNA-Seq Data Analysis

Small RNA-Seq Data Analysis Introduction
Turn-around Time


Short non-coding RNA molecules such as microRNA have been recognized as key players in many basic pathways and next-generation sequencing makes it possible to rapidly and cost-effectively to analyze known and novel small RNA.

Small RNA-Seq involves a unique library preparation process to enrich small RNA fragments (18-40 nt), which will eliminate most full-length mRNA molecules.

Small RNA-Seq usually focuses on characterizing microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small nucleolar RNA (snoRNAs) and small interfering RNAs (siRNA). Small RNA-Seq data analysis requires a reference genome sequence. The analysis will be limited to comparison to known small RNA molecules without a reference sequence.


Following is a list of common analysis items for small RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project.

1) Experiment design consultation
2) Data QC, adaptor removal, and size selection
3) Read characterization by mapping to a reference genome sequence, known RNA families (e.g., Rfam), and known microRNA sequences (e.g., miRBase)
4) Novel microRNA prediction
5) Expression quantitation of known and novel microRNA
6) Differential expression analysis of known and novel microRNA
7) Target gene prediction and network/pathway analysis
8) Written project report with analysis methods, publication-ready graphics, and references

Turn-around Time

Upon data receipt, we usually finish a typical small RNA-Seq analysis project in 2-3 days. The actual turn-around time, however, is highly dependent on sample number, data amount, and project complexity.


Publications below are representative research or review papers that will help you understand how small RNA-Seq is employed in biomedical research.

  • Creighton, C. et al. (2009) Expression profiling of microRNAs by deep sequencing. Briefings in Bioinformatics. Vol. 10- No. 5 (490-497).


What kind of reads should I use for small RNA-Seq?
Small RNA-Seq characterizes RNA fragment of 18-40bp. We recommend 36-bp single-end reads.
Why is the 3' adaptor sequence required for small RNA-Seq data analysis? How do I obtain this information?
It is important to remove any 3' adaptor sequence from the sequencing reads before any small RNA data analysis. Please ask your next-generation sequencing provider/facility for the exact sequence of 3' adaptor used in the library construction steps.