**Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity Livestock Species: Elucidating the Ambiguity**

**Transcriptome Analysis of Non‐Coding RNAs in** 

DOI: 10.5772/intechopen.69872

Duy N. Do, Pier-Luc Dudemaine, Bridget Fomenky and Eveline M. Ibeagha-Awemu Fomenky and Eveline M. Ibeagha-Awemu Additional information is available at the end of the chapter

Additional information is available at the end of the chapter

Duy N. Do, Pier-Luc Dudemaine, Bridget

http://dx.doi.org/10.5772/intechopen.69872

#### **Abstract**

The recent remarkable development of transcriptomics technologies, especially next generation sequencing technologies, allows deeper exploration of the hidden landscapes of complex traits and creates great opportunities to improve livestock productivity and welfare. Non-coding RNAs (ncRNAs), RNA molecules that are not translated into proteins, are key transcriptional regulators of health and production traits, thus, transcriptomics analyses of ncRNAs are important for a better understanding of the regulatory architecture of livestock phenotypes. In this chapter, we present an overview of common frameworks for generating and processing RNA sequence data to obtain ncRNA transcripts. Then, we review common approaches for analyzing ncRNA transcriptome data and present current state of the art methods for identification of ncRNAs and functional inference of identified ncRNAs, with emphasis on tools for livestock species. We also discuss future challenges and perspectives for ncRNA transcriptome data analysis in livestock species.

**Keywords:** bioinformatics, genome editing, livestock species, long non-coding RNA, noncoding RNA, microRNA, transcriptome
