Computational methods for mapping, assembly and quantification for coding and non-coding transcripts

Isaac A. Babarinde, Yuhao Li, Andrew P. Hutchins
2019 Computational and Structural Biotechnology Journal  
The measurement of gene expression has long provided significant insight into biological functions. The development of high-throughput short-read sequencing technology has revealed transcriptional complexity at an unprecedented scale, and informed almost all areas of biology. However, as researchers have sought to gather more insights from the data, these new technologies have also increased the computational analysis burden. In this review, we describe typical computational pipelines for
more » ... q analysis and discuss their strengths and weaknesses for the assembly, quantification and analysis of coding and non-coding RNAs. We also discuss the assembly of transposable elements into transcripts, and the difficulty these repetitive elements pose. In summary, RNA-Seq is a powerful technology that is likely to remain a key asset in the biologist's toolkit.
doi:10.1016/j.csbj.2019.04.012 pmid:31193391 pmcid:PMC6526290 fatcat:lpfymy2zebc5lf7bs4m356wdzi