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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li, Colin N Dewey
2011 BMC Bioinformatics  
Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes.  ...  RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms.  ...  Acknowledgements and Funding We thank Victor Ruotti, Ron Stewart, Angela Elwell, and Jennifer Bolin for feedback on the software and for valuable discussions regarding RNA-Seq protocols.  ... 
doi:10.1186/1471-2105-12-323 pmid:21816040 pmcid:PMC3163565 fatcat:27tkrqbmjrfctnhmodskvwhhqa

RSEM [chapter]

Bo Li, Colin Dewey
2014 Bioinformatics  
Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes.  ...  RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms.  ...  Acknowledgements and Funding We thank Victor Ruotti, Ron Stewart, Angela Elwell, and Jennifer Bolin for feedback on the software and for valuable discussions regarding RNA-Seq protocols.  ... 
doi:10.1201/b16589-5 fatcat:pgom6fqufjhr3e5d5ztwr7t65a

Analysis of Whole Transcriptome Sequencing Data: Workflow and Software

In Seok Yang, Sangwoo Kim
2015 Genomics & Informatics  
In this review, we introduce routine RNA-seq workflow together with related software, focusing particularly on transcriptome reconstruction and expression quantification.  ...  RNA-seq is a powerful technique for characterizing and quantifying the transcriptome and accelerates the development of bioinformatics software.  ...  We discuss each isoform-level quantification method in detail in the following sections. RSEM RSEM is software that quantifies transcript-level abundance from RNA-seq data.  ... 
doi:10.5808/gi.2015.13.4.119 pmid:26865842 pmcid:PMC4742321 fatcat:y4q3sgeckbbpdmcgnpmakhlvku

Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq

Peng Liu, Rajendran Sanalkumar, Emery H. Bresnick, Sündüz Keleş, Colin N. Dewey
2016 Genome Research  
To improve quantification accuracy in such difficult cases, we developed a novel computational method, prior-enhanced RSEM (pRSEM), which uses a complementary data type in addition to RNA-seq data.  ...  Despite its successes, isoform-level quantification remains difficult because short RNA-seq reads are often compatible with multiple alternatively spliced isoforms.  ...  Alexander Dobin for sharing the RAMPAGE alignment data.  ... 
doi:10.1101/gr.199174.115 pmid:27405803 pmcid:PMC4971760 fatcat:li7xl77v6bc7dhkifspzxh4olu

An RNA-Seq Protocol for Differential Expression Analysis

Nick D.L. Owens, Elena De Domenico, Michael J. Gilchrist
2019 Cold Spring Harbor Protocols  
Here we present a standard RNA-Seq protocol for performing two-state differential gene expression analysis (between groups of replicates of control and treated embryos) using Illumina sequencing.  ...  Here we consider RNA-Seq, used to measure global gene expression through RNA fragmentation, capture, sequencing, and subsequent computational analysis.  ...  Mapping to a reference genome can be performed with or without aid from reference gene models.  ... 
doi:10.1101/pdb.prot098368 pmid:30952685 fatcat:2il3bpf2hraxdguvpxh5iu4vbe

Leveraging transcript quantification for fast computation of alternative splicing profiles [article]

Gael P Alamancos, Amadís Pagès, Juan L Trincado, Nicolás Bellora, Eduardo Eyras
2014 bioRxiv   pre-print
Coupled with fast transcript quantification, SUPPA provides inclusion values at a much higher speed than existing methods without compromising accuracy, thereby facilitating the systematic splicing analysis  ...  High-throughput RNA sequencing allows genome-wide analyses of splicing across multiple conditions.  ...  Xing for useful discussions and for sharing sequencing and RT-PCR data.  ... 
doi:10.1101/008763 fatcat:nm2ckmgqs5gv5i7uyq2v5vpsqe

Leveraging transcript quantification for fast computation of alternative splicing profiles

Gael P. Alamancos, Amadís Pagès, Juan L. Trincado, Nicolás Bellora, Eduardo Eyras
2015 RNA: A publication of the RNA Society  
Coupled with fast transcript quantification, SUPPA provides inclusion values at a much higher speed than existing methods without compromising accuracy, thereby facilitating the systematic splicing analysis  ...  High-throughput RNA sequencing allows genome-wide analyses of splicing across multiple conditions.  ...  Xing for useful discussions and for sharing sequencing and RT-PCR data.  ... 
doi:10.1261/rna.051557.115 pmid:26179515 pmcid:PMC4536314 fatcat:tj3tbtl2zvdmpdzx7psvc44j2q

Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data

Yasunobu Okamura, Kengo Kinoshita
2018 BMC Bioinformatics  
Here, we propose a novel method, Matataki, for rapidly estimating gene expression levels from RNA-Seq data.  ...  Data generated by RNA sequencing (RNA-Seq) is now accumulating in vast amounts in public repositories, especially for human and mouse genomes.  ...  Acknowledgements The super-computing resource was provided by Human Genome Center of the University of Tokyo. Availability of data and materials Not applicable.  ... 
doi:10.1186/s12859-018-2279-y pmid:30012088 pmcid:PMC6048772 fatcat:62iwtyxv7zfwjivveetjv7vjai

Comparative evaluation of full-length isoform quantification from RNA-Seq [article]

Dimitra Sarantopoulou, Soumyashant Nayak, Thomas G Brooks, Nicholas F Lahens, Gregory R R Grant
2019 bioRxiv   pre-print
Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and an area of active development.  ...  The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA-Seq reads are typically short.  ...  A set of reference transcript sequences was built using rsem-prepare-reference script based on the GRCm38 Ensemblv75 reference genome and the corresponding transcript annotation file.  ... 
doi:10.1101/698605 fatcat:oyli3dixlncsjp3hem7nqj3jby

An approach for assessing RNA-seq quantification algorithms in replication studies

Po-Yen Wu, John H. Phan, May D. Wang
2013 2013 IEEE International Workshop on Genomic Signal Processing and Statistics  
A single RNA-seq run can produce millions of sequence reads. Focusing on RNA-seq transcriptome profiling, a standard data analysis pipeline includes sequence reads alignment,  ...  Examining the normalized root-meansquare error, the percentage error of the coefficient of variation, and the distribution of the coefficient of variation, we found that quantification algorithms with  ...  Transcript-level performance metrics for simulated RNA-seq data. Metrics are the same as those in Figure 2 .  ... 
doi:10.1109/gensips.2013.6735918 pmid:27525167 pmcid:PMC4981182 dblp:conf/gensips/WuPW13 fatcat:sl3dkeleebfmzhvtrvj2ddij2e

TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads

Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Masao Nagasaki
2014 BMC Genomics  
Conclusions: TIGAR2 is a sensitive and accurate tool for quantifying transcript isoform abundances from RNA-Seq data.  ...  Results: We propose TIGAR2, a statistical method for quantifying transcript isoforms from fixed and variable length RNA-Seq data.  ...  This article has been published as part of BMC Genomics Volume 15 Supplement 10, 2014: Proceedings of the 25th International Conference on Genome Informatics (GIW/ISCB-Asia): Genomics.  ... 
doi:10.1186/1471-2164-15-s10-s5 pmid:25560536 pmcid:PMC4304212 fatcat:d76hvdg7bngpxlij34i7sgwbgm

Computational methods for mapping, assembly and quantification for coding and non-coding transcripts

Isaac A. Babarinde, Yuhao Li, Andrew P. Hutchins
2019 Computational and Structural Biotechnology Journal  
In summary, RNA-Seq is a powerful technology that is likely to remain a key asset in the biologist's toolkit.  ...  In this review, we describe typical computational pipelines for RNA-Seq analysis and discuss their strengths and weaknesses for the assembly, quantification and analysis of coding and non-coding RNAs.  ...  Gene-level and Transcript-level Quantification At the simplest level of analysis, RNA-Seq data can be considered by mapping it only against a reference transcriptome (not the genome).  ... 
doi:10.1016/j.csbj.2019.04.012 pmid:31193391 pmcid:PMC6526290 fatcat:lpfymy2zebc5lf7bs4m356wdzi

WemIQ: an accurate and robust isoform quantification method for RNA-seq data

Jing Zhang, C.-C. Jay Kuo, Liang Chen
2014 Computer applications in the biosciences : CABIOS  
For the recent single-cell RNA-seq data, WemIQ also provides the opportunity to distinguish bias heterogeneity from true biological heterogeneity and uncovers smaller cell-to-cell expression variability  ...  The weight represents the oversampling or undersampling of sequence reads and is estimated through a generalized Poisson model without any presumption on the bias sources and formats.  ...  However, the accurate estimation of transcript isoform expression from RNA-seq data remains a challenge.  ... 
doi:10.1093/bioinformatics/btu757 pmid:25406327 pmcid:PMC4380033 fatcat:yh3xiyqpqrdxpbwogskapsyjoa

CRSP: Comparative RNA-seq pipeline for species lacking both of sequenced genomes and reference transcripts [article]

Atefeh Bagheri, Colin Dewey, Ron Stewart, Peng Jiang
2022 bioRxiv   pre-print
However, typical RNA-seq data analysis pipelines depend on either a sequenced genome or reference transcripts.  ...  To solve this problem, we developed CRSP, an RNA-seq pipeline integrating multiple comparative species strategy but not depending on a specific sequenced genome or reference transcripts.  ...  Current RNA-seq tools either rely on an annotated reference genome or reference transcripts (e.g., RSEM).  ... 
doi:10.1101/2022.02.04.479193 fatcat:iolbay7fczgx3jumjjayzcg7fy

Comparative evaluation of full-length isoform quantification from RNA-Seq

Dimitra Sarantopoulou, Thomas G. Brooks, Soumyashant Nayak, Antonijo Mrčela, Nicholas F. Lahens, Gregory R. Grant
2021 BMC Bioinformatics  
The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA-Seq reads are short.  ...  Background Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning.  ...  The data were aligned to the reference genome or transcriptome with STAR [19] and quantified with the seven methods.  ... 
doi:10.1186/s12859-021-04198-1 pmid:34034652 fatcat:r7mqsoisi5dj5llq2wrjh4k2pq
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