Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data
نویسندگان
چکیده
منابع مشابه
A Robust Method for Transcript Quantification with RNA-seq Data
The advent of high throughput RNA-seq technology allows deep sampling of the transcriptome, making it possible to characterize both the diversity and the abundance of transcript isoforms. Accurate abundance estimation or transcript quantification of isoforms is critical for downstream differential analysis (e.g., healthy vs. diseased cells) but remains a challenging problem for several reasons....
متن کاملWemIQ: an accurate and robust isoform quantification method for RNA-seq data
MOTIVATION The deconvolution of isoform expression from RNA-seq remains challenging because of non-uniform read sampling and subtle differences among isoforms. RESULTS We present a weighted-log-likelihood expectation maximization method on isoform quantification (WemIQ). WemIQ integrates an effective bias removal with a weighted expectation maximization (EM) algorithm to distribute reads amon...
متن کاملGene expression WemIQ: an accurate and robust isoform quantification method for RNA-seq data
Motivation: The deconvolution of isoform expression from RNA-seq remains challenging because of non-uniform read sampling and subtle differences among isoforms. Results: We present a weighted-log-likelihood expectation maximization method on isoform quantification (WemIQ). WemIQ integrates an effective bias removal with a weighted expectation maximization (EM) algorithm to distribute reads amon...
متن کاملSalmon: Accurate, Versatile and Ultrafast Quantification from RNA-seq Data using Lightweight-Alignment
Transcript quantification is a central task in the analysis of RNA-seq data. Accurate computational methods for the quantification of transcript abundances are essential for downstream analysis. However, most existing approaches are much slower than is necessary for their degree of accuracy. We introduce Salmon, a novel method and software tool for transcript quantification that exhibits state-...
متن کاملComputational Pipeline for Human Transcriptome Quantification Using RNA-seq Data
Acknowledgments First and foremost, I want to thank my advisor Dr. Dongxiao Zhu. His endless support and wisdom helped me to finish this thesis. His enthusiasm for Bioinformatics was contagious—and I definitely caught it. His depth of knowledge and very precise academic guidance brought me to develop a computational pipeline for characterizing human transcriptome using RNA-seq. I would like to ...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2018
ISSN: 1471-2105
DOI: 10.1186/s12859-018-2279-y