Cargando…

CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data

The fundamental task in RNA-Seq-based transcriptome analysis is alignment of millions of short reads to the reference genome or transcriptome. Choosing the right tool for the dataset in hand from many existent RNA-Seq alignment packages remains a critical challenge for downstream analysis. To facili...

Descripción completa

Detalles Bibliográficos
Autores principales:	Kumar, Praveen Kumar Raj, Hoang, Thanh V., Robinson, Michael L., Tsonis, Panagiotis A., Liang, Chun
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group 2015
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4548254/ https://www.ncbi.nlm.nih.gov/pubmed/26304587 http://dx.doi.org/10.1038/srep13443

Ejemplares similares

Comparative transcriptome analysis of epithelial and fiber cells in newborn mouse lenses with RNA sequencing
por: Hoang, Thanh V., et al.
Publicado: (2014)

Evaluation of tools for long read RNA-seq splice-aware alignment
por: Križanović, Krešimir, et al.
Publicado: (2018)

Supersplat—spliced RNA-seq alignment
por: Bryant, Douglas W., et al.
Publicado: (2010)

Systematic evaluation of spliced alignment programs for RNA-seq data
por: Engström, Pär G, et al.
Publicado: (2013)

ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
por: Denti, Luca, et al.
Publicado: (2018)

iMapSplice: Alleviating reference bias through personalized RNA-seq alignment
por: Liu, Xinan, et al.
Publicado: (2018)

Limitations of alignment-free tools in total RNA-seq quantification
por: Wu, Douglas C., et al.
Publicado: (2018)

Systematic evaluation of differential splicing tools for RNA-seq studies
por: Mehmood, Arfa, et al.
Publicado: (2019)

HSA: A Heuristic Splice Alignment Tool
por: Bu, Jingde, et al.
Publicado: (2013)

SeqTools: visual tools for manual analysis of sequence alignments
por: Barson, Gemma, et al.
Publicado: (2016)

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns
por: Langenberger, David, et al.
Publicado: (2012)

FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions
por: Gatto, Alberto, et al.
Publicado: (2014)

Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach
por: Zhang, Yi, et al.
Publicado: (2018)

Modelling and simulating generic RNA-Seq experiments with the flux simulator
por: Griebel, Thasso, et al.
Publicado: (2012)

Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data
por: Ding, Lizhong, et al.
Publicado: (2017)

scAlign: a tool for alignment, integration, and rare cell identification from scRNA-seq data
por: Johansen, Nelson, et al.
Publicado: (2019)

ARH-seq: identification of differential splicing in RNA-seq data
por: Rasche, Axel, et al.
Publicado: (2014)

Alignment strategy for different types of varus knee with generic instruments: Mechanical alignment or kinematic alignment?
por: Lin, Haoran, et al.
Publicado: (2023)

SeqAn An efficient, generic C++ library for sequence analysis
por: Döring, Andreas, et al.
Publicado: (2008)

Comparative Analyses between Retained Introns and Constitutively Spliced Introns in Arabidopsis thaliana Using Random Forest and Support Vector Machine
por: Mao, Rui, et al.
Publicado: (2014)

Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq
por: Hartley, Stephen W., et al.
Publicado: (2016)

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts
por: Ryan, Michael C., et al.
Publicado: (2012)

SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups
por: Jammali, Safa, et al.
Publicado: (2019)

Fugacium Spliced Leader Genes Identified from Stranded RNA-Seq Datasets
por: Song, Yue, et al.
Publicado: (2019)

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
por: Wang, Kai, et al.
Publicado: (2010)

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq
por: Hu, Yin, et al.
Publicado: (2013)

Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs
por: LeGault, Laura H., et al.
Publicado: (2013)

3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists
por: Guo, Wenbin, et al.
Publicado: (2020)

HMMSplicer: A Tool for Efficient and Sensitive Discovery of Known and Novel Splice Junctions in RNA-Seq Data
por: Dimon, Michelle T., et al.
Publicado: (2010)

Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data
por: Zhou, Ao, et al.
Publicado: (2012)

MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data
por: Green, Christopher J, et al.
Publicado: (2018)

RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts
por: Sorber, Katherine, et al.
Publicado: (2011)

MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies
por: Kumar, Pankaj, et al.
Publicado: (2015)

TopHat: discovering splice junctions with RNA-Seq
por: Trapnell, Cole, et al.
Publicado: (2009)

Mapping Splicing Quantitative Trait Loci in RNA-Seq
por: Jia, Cheng, et al.
Publicado: (2014)

Mapping Splicing Quantitative Trait Loci in RNA-Seq
por: Jia, Cheng, et al.
Publicado: (2015)

TrueSight: a new algorithm for splice junction detection using RNA-seq
por: Li, Yang, et al.
Publicado: (2013)

Detection of splice junctions from paired-end RNA-seq data by SpliceMap
por: Au, Kin Fai, et al.
Publicado: (2010)

Accurate spliced alignment of long RNA sequencing reads
por: Sahlin, Kristoffer, et al.
Publicado: (2021)

Detection of aberrant splicing events in RNA-seq data using FRASER
por: Mertes, Christian, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_3bltg2cs71mk9taidf51snp3tf