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RNA-Seq: revelation of the messengers [PDF]
Trends in Plant Science, 2013 Next-generation RNA-sequencing (RNA-Seq) is rapidly outcompeting microarrays as the technology of choice for whole-transcriptome studies. However, the bioinformatics skills required for RNA-Seq data analysis often pose a significant hurdle for many biologists.
Van Verk +6 more
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An RNA-seq primer for pulmonologists [PDF]
European Respiratory Journal, 2019 With the evolution of high throughput sequencing technologies, the past decade has seen an exponential rise in the use of RNA sequencing (RNA-seq). RNA-seq has deepened our understanding of biological systems to unprecedented levels of resolution, identifying not only gene expression signatures but also regulatory RNA molecules that may play critical ...
Sarah G. Chu +3 more
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Bioinformatics, 2011 Abstract Summary: RNA-Seq is an exciting methodology that leverages the power of high-throughput sequencing to measure RNA transcript counts at an unprecedented accuracy. However, the data generated from this process are extremely large and biologist-friendly tools with which to analyze it are sorely lacking. MultiExperiment Viewer (MeV)
Eleanor Howe +3 more
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Uncovering the Complexity of Transcriptomes with RNA-Seq [PDF]
Journal of Biomedicine and Biotechnology, 2010 In recent years, the introduction of massively parallel sequencing platforms for Next Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred thousand DNA fragments, dramatically changed the landscape of the genetics studies.
Costa V +3 more
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RNA-Seq Assembly – Are We There Yet? [PDF]
Frontiers in Plant Science, 2012 Transcriptomic sequence resources represent invaluable assets for research, in particular for non-model species without a sequenced genome. To date, the Next Generation Sequencing technologies 454/Roche and Illumina have been used to generate transcriptome sequence databases by mRNA-Seq for more than fifty different plant species.
Schliesky, Simon +3 more
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Supersplat—spliced RNA-seq alignment [PDF]
Bioinformatics, 2010 Abstract Motivation: High-throughput sequencing technologies have recently made deep interrogation of expressed transcript sequences practical, both economically and temporally. Identification of intron/exon boundaries is an essential part of genome annotation, yet remains a challenge.
Douglas W. Bryant Jr. +4 more
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Improving RNA-Seq Precision with MapAl [PDF]
Frontiers in Genetics, 2012 With currently available RNA-Seq pipelines, expression estimates for most genes are very noisy. We here introduce MapAl, a tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. In the post-processing of RNA-Seq reads, it incorporates gene models already at the stage of read alignment, increasing the number ...
Paweł P Łabaj +4 more
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RNA‐Seq for Bacterial Gene Expression [PDF]
Current Protocols in Nucleic Acid Chemistry, 2018 AbstractRNA sequencing (RNA‐seq) has become the preferred method for global quantification of bacterial gene expression. With the continued improvements in sequencing technology and data analysis tools, the most labor‐intensive and expensive part of an RNA‐seq experiment is the preparation of sequencing libraries, which is also essential for the ...
Poulsen, Line Dahl, Vinther, Jeppe
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The Comparison between Bulk RNA-seq and Ssingle-cell RNA-seq
Journal of Physics: Conference Series, 2021 Abstract Bulk RNA-seq and single cell RNA-seq (Sc-RNA) seq are two well-known methods and are broadly used in biology areas. Even though the two ways are all starting from the mRNA level to do the transcriptional analysis, many differences still show in them, but the differences which are critical for researchers to judge and consider ...
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