TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads

TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads

Bibliographic Details
Main Authors:	Mangul, Serghei, Caciula, Adrian, Brinza, Dumitru, Mandoiu, Ion I, Zelikovsky, Alex
Format:	Online
Language:	English
Published:	BioMed Central 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522042/

Similar Items

Transcriptome assembly and quantification from Ion Torrent RNA-Seq data
by: Mangul, Serghei, et al.
Published: (2014)

Estimation of alternative splicing isoform frequencies from RNA-Seq data
by: Nicolae, Marius, et al.
Published: (2011)

Inferring viral quasispecies spectra from 454 pyrosequencing reads
by: Astrovskaya, Irina, et al.
Published: (2011)

Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates
by: Al Seesi, Sahar, et al.
Published: (2014)

Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows
by: Skums, Pavel, et al.
Published: (2013)

Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire
by: Ekaterina Gerasimov, et al.
Published: (2017-06-01)

ILP-based maximum likelihood genome scaffolding
by: Lindsay, James, et al.
Published: (2014)

Single cell RNA-seq data clustering using TF-IDF based methods
by: Marmar Moussa, et al.
Published: (2018-08-01)

Inferring metabolic pathway activity levels from RNA-Seq data
by: Temate-Tiagueu, Yvette, et al.
Published: (2016)

Accurate viral population assembly from ultra-deep sequencing data
by: Mangul, Serghei, et al.
Published: (2014)

Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA
by: Sengupta, Srikumar, et al.
Published: (2011)

Guest Editors' Introduction
by: Chen, Jianer, et al.
Published: (2012)

CLASS: constrained transcript assembly of RNA-seq reads
by: Song, Li, et al.
Published: (2013)

Assessment of transcript reconstruction methods for RNA-seq
by: Steijger, Tamara, et al.
Published: (2013)

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data
by: Jia, Wenlong, et al.
Published: (2013)

Analysis of paired end Pol II ChIP-seq and short capped RNA-seq in MCF-7 cells
by: Scheidegger, Adam, et al.
Published: (2015)

DELLY: structural variant discovery by integrated paired-end and split-read analysis
by: Rausch, Tobias, et al.
Published: (2012)

SeqPurge: highly-sensitive adapter trimming for paired-end NGS data
by: Sturm, Marc, et al.
Published: (2016)

Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data
by: Liu, Silvia, et al.
Published: (2016)

Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-seq
by: Huang, Yan, et al.
Published: (2014)

Differential expression analysis for paired RNA-seq data
by: Chung, Lisa M, et al.
Published: (2013)

To Moscow with Love: Partial Reconstruction of Vygotsky’s Trip to London
by: van der Veer, René, et al.
Published: (2011)

Meraculous: De Novo Genome Assembly with Short Paired-End Reads
by: Chapman, Jarrod A., et al.
Published: (2011)

Accurate indel prediction using paired-end short reads
by: Grimm, Dominik, et al.
Published: (2013)

Inferring short tandem repeat variation from paired-end short reads
by: Cao, Minh Duc, et al.
Published: (2014)

Misassembly detection using paired-end sequence reads and optical mapping data
by: Muggli, Martin D., et al.
Published: (2015)

Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols
by: Susan M. Corley, et al.
Published: (2017-05-01)

Reconstructing cancer genomes from paired-end sequencing data
by: Oesper, Layla, et al.
Published: (2012)

A Genetic Algorithm for Diploid Genome Reconstruction Using Paired-End Sequencing
by: Ting, Chuan-Kang, et al.
Published: (2016)

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
by: Sboner, Andrea, et al.
Published: (2010)

PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data
by: Zhang, Yanju, et al.
Published: (2012)

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq
by: Liu, Chenglin, et al.
Published: (2013)

Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development
by: Karunakaran, Devi Krishna Priya, et al.
Published: (2016)

Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments
by: Lu, Zhipeng, et al.
Published: (2014)

HLA typing from RNA-Seq sequence reads
by: Boegel, Sebastian, et al.
Published: (2012)

CRAC: an integrated approach to the analysis of RNA-seq reads
by: Philippe, Nicolas, et al.
Published: (2013)

MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing
by: Parikh, Hardik I., et al.
Published: (2016)

A paired-end sequencing strategy to map the complex landscape of transcription initiation
by: Ni, Ting, et al.
Published: (2010)

High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)
by: Preston, Jessica L., et al.
Published: (2016)

Effect of RNA integrity on uniquely mapped reads in RNA-Seq
by: Chen, Emily A, et al.
Published: (2014)