**Transcriptome Analysis for Non-Model Organism: Current Status and Best-Practices**

Vahap Eldem, Gokmen Zararsiz, Tunahan Taşçi, Izzet Parug Duru, Yakup Bakir and Melike Erkan

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/intechopen.68983

#### **Abstract**

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54 Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

Since transcriptome analysis provides genome-wide sequence and gene expression information, transcript reconstruction using RNA-Seq sequence reads has become popular during recent years. For non-model organism, as distinct from the reference genome-based mapping, sequence reads are processed via *de novo* transcriptome assembly approaches to produce large numbers of contigs corresponding to coding or non-coding, but expressed, part of genome. In spite of immense potential of RNA-Seq–based methods, particularly in recovering full-length transcripts and spliced isoforms from short-reads, the accurate results can be only obtained by the procedures to be taken in a step-by-step manner. In this chapter, we aim to provide an overview of the state-of-the-art methods including (i) quality check and pre-processing of raw reads, (ii) the pros and cons of *de novo* transcriptome assemblers, (iii) generating non-redundant transcript data, (iv) current quality assessment tools for *de novo* transcriptome assemblies, (v) approaches for transcript abundance and differential expression estimations and finally (vi) further mining of transcriptomic data for particular biological questions. Our intention is to provide an overview and practical guidance for choosing the appropriate approaches to best meet the needs of researchers in this area and also outline the strategies to improve on-going projects.

**Keywords:** whole transcriptome, *de novo* assembly, genome-wide expression, non-model organism
