Abstract
RNA-Seq has become a routine strategy for genome-wide gene expression comparisons in bacteria. Despite lower resolution in transcript border parsing compared with dRNA-Seq, TSS-EMOTE, Cappable-seq, Term-seq, and others, directional RNA-Seq still illustrates its advantages: low cost, quantification and transcript border analysis with a medium resolution (±10–20 nt). To facilitate mining of directional RNA-Seq datasets especially with respect to transcript structure analysis, we developed a tool, TrBorderExt, which can parse transcript start sites and termination sites accurately in bacteria. A detailed protocol is described in this chapter for how to use the software package step by step to identify bacterial transcript borders from raw RNA-Seq data. The package was developed with Perl and R programming languages, and is accessible freely through the website: http://www.szu-bioinf.org/TrBorderExt.
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Acknowledgment
This work was supported by a Natural Science Funding of Shenzhen (JCYJ201607115221141) and a Shenzhen Peacock Plan fund (827-000116) to YW. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Wang, Y., Sun, Ma., White, A.P. (2018). RNA-Seq-Based Transcript Structure Analysis with TrBorderExt. In: Wang, Y., Sun, Ma. (eds) Transcriptome Data Analysis. Methods in Molecular Biology, vol 1751. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7710-9_6
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DOI: https://doi.org/10.1007/978-1-4939-7710-9_6
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