How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets
The sequencing of the full transcriptome (RNA-seq) has become the preferred choice for the
measurement of genome-wide gene expression. Despite its widespread use, challenges …
measurement of genome-wide gene expression. Despite its widespread use, challenges …
[HTML][HTML] Trimming of sequence reads alters RNA-Seq gene expression estimates
Abstract Background High-throughput RNA-Sequencing (RNA-Seq) has become the
preferred technique for studying gene expression differences between biological samples …
preferred technique for studying gene expression differences between biological samples …
[HTML][HTML] A scaling normalization method for differential expression analysis of RNA-seq data
MD Robinson, A Oshlack - Genome biology, 2010 - Springer
The fine detail provided by sequencing-based transcriptome surveys suggests that RNA-seq
is likely to become the platform of choice for interrogating steady state RNA. In order to …
is likely to become the platform of choice for interrogating steady state RNA. In order to …
End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data
A Derr, C Yang, R Zilionis, A Sergushichev… - Genome …, 2016 - genome.cshlp.org
RNA-seq protocols that focus on transcript termini are well suited for applications in which
template quantity is limiting. Here we show that, when applied to end-sequencing data …
template quantity is limiting. Here we show that, when applied to end-sequencing data …
RNA‐seq data: challenges in and recommendations for experimental design and analysis
RNA‐seq is widely used to determine differential expression of genes or transcripts as well
as identify novel transcripts, identify allele‐specific expression, and precisely measure …
as identify novel transcripts, identify allele‐specific expression, and precisely measure …
[HTML][HTML] Technical variations in low-input RNA-seq methodologies
Recent advances in RNA-seq methodologies from limiting amounts of mRNA have
facilitated the characterization of rare cell-types in various biological systems. So far …
facilitated the characterization of rare cell-types in various biological systems. So far …
RNA sequencing: the teenage years
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for
transcriptome-wide analysis of differential gene expression and differential splicing of …
transcriptome-wide analysis of differential gene expression and differential splicing of …
[HTML][HTML] The impact of amplification on differential expression analyses by RNA-seq
Currently, quantitative RNA-seq methods are pushed to work with increasingly small starting
amounts of RNA that require amplification. However, it is unclear how much noise or bias …
amounts of RNA that require amplification. However, it is unclear how much noise or bias …
Design and validation issues in RNA-seq experiments
Z Fang, X Cui - Briefings in bioinformatics, 2011 - academic.oup.com
The next-generation sequencing technologies are being rapidly applied in biological
research. Tens of millions of short sequences generated in a single experiment provide us …
research. Tens of millions of short sequences generated in a single experiment provide us …
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
De novo assembly of RNA-seq data enables researchers to study transcriptomes without the
need for a genome sequence; this approach can be usefully applied, for instance, in …
need for a genome sequence; this approach can be usefully applied, for instance, in …