A comparison between whole transcript and 3' RNA sequencing methods using Kapa and Lexogen library preparation methods. [PDF]
, 2019 Background3' RNA sequencing provides an alternative to whole transcript analysis. However, we do not know a priori the relative advantage of each method.
Fuqua, Brie K +6 more
core +1 more source
PLoS ONE, 2019 The wealth of information deliverable from transcriptome sequencing (RNA-seq) is significant, however current applications for variant detection still remain a challenge due to the complexity of the transcriptome.
Modupeore O Adetunji +3 more
doaj +1 more source
Comparison of reproducibility, accuracy, sensitivity, and specificity of miRNA quantification platforms [PDF]
, 2019 Given the increasing interest in their use as disease biomarkers, the establishment of reproducible, accurate, sensitive, and specific platforms for microRNA (miRNA) quantification in biofluids is of high priority.
Barczak, Andrea J +8 more
core +1 more source
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
openaire +3 more sources
Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability. [PDF]
PLoS ONE, 2015 Rapidly growing public gene expression databases contain a wealth of data for building an unprecedentedly detailed picture of human biology and disease.
Karolis Uziela, Antti Honkela
doaj +1 more source
Near-optimal RNA-Seq quantification [PDF]
, 2015 We present a novel approach to RNA-Seq quantification that is near optimal in speed and accuracy. Software implementing the approach, called kallisto, can be used to analyze 30 million unaligned paired-end RNA-Seq reads in less than 5 minutes on a ...
Bray, Nicolas +3 more
core +1 more source
Simultaneous generation of many RNA-seq libraries in a single reaction [PDF]
, 2015 Although RNA-seq is a powerful tool, the considerable time and cost associated with library construction has limited its utilization for various applications.
Bhattacharyya, Roby P. +15 more
core +1 more source
COEX-Seq: Convert a Variety of Measurements of Gene Expression in RNA-Seq [PDF]
Genomics & Informatics, 2018 Next generation sequencing (NGS), a high-throughput DNA sequencing technology, is widely used for molecular biological studies. In NGS, RNA-sequencing (RNA-Seq), which is a short-read massively parallel sequencing, is a major quantitative transcriptome ...
Sang Cheol Kim +2 more
doaj +1 more source
COLOMBOS v2.0 : an ever expanding collection of bacterial expression compendia [PDF]
, 2013 The COLOMBOS database (http://www.colombos.net) features comprehensive organism-specific cross-platform gene expression compendia of several bacterial model organisms and is supported by a fully interactive web portal and an extensive web API.
Bianco, Luca +11 more
core +1 more source
SPsimSeq : semi-parametric simulation of bulk and single-cell RNA-sequencing data [PDF]
, 2020 SPsimSeq is a semi-parametric simulation method to generate bulk and single-cell RNA-sequencing data. It is designed to simulate gene expression data with maximal retention of the characteristics of real data.
Assefa, Alemu Takele +2 more
core +1 more source