Limitations of alignment-free tools in total RNA-seq quantification
نویسندگان
چکیده
منابع مشابه
Supersplat—spliced RNA-seq alignment
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. Here, we present supersplat, a method for unbiased splice-junction discovery through empirical RNA-seq data. RESULTS U...
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Nicolas L. Bray, Harold Pimentel, Páll Melsted and Lior Pachter*, 1. Innovative Genomics Initiative, UC Berkeley 2. Department of Computer Science, UC Berkeley 3. Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland 4. Departments of Mathematics and Molecular & Cell Biology, UC Berkeley * Corresponding author: [email protected] We presen...
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Background: The stress is one of main factors effects on production system. Several factors (both genetic and environmental elements) regulate immune response to stress. Objectives: In order to determine the major immune system regulatory genes underlying stress responses, a learning Bayesian network approach for those regulatory genes was applied to RNA-...
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RNA-Seq is rapidly becoming the standard technology for transcriptome analysis. Fundamental to many of the applications of RNA-Seq is the quantification problem, which is the accurate measurement of relative transcript abundances from the sequenced reads. We focus on this problem, and review many recently published models that are used to estimate the relative abundances. In addition to describ...
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RNA-Seq makes it possible not only to measure gene expression but also to identify and quantify transcript isoforms in different experimental conditions. Although a large number of tools allow to infer isoform expression levels from RNA-Seq data, the quantification of alternative splicing variants remains challenging. Aligning reads that span (possibly un-annotated) exon-exon junctions in an ef...
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ژورنال
عنوان ژورنال: BMC Genomics
سال: 2018
ISSN: 1471-2164
DOI: 10.1186/s12864-018-4869-5