Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
Published 2016 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
Authors
Keywords
-
Journal
Nature Protocols
Volume 11, Issue 9, Pages 1650-1667
Publisher
Springer Nature
Online
2016-08-25
DOI
10.1038/nprot.2016.095
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
- (2015) Mihaela Pertea et al. NATURE BIOTECHNOLOGY
- Ballgown bridges the gap between transcriptome assembly and expression analysis
- (2015) Alyssa C Frazee et al. NATURE BIOTECHNOLOGY
- HISAT: a fast spliced aligner with low memory requirements
- (2015) Daehwan Kim et al. NATURE METHODS
- Orchestrating high-throughput genomic analysis with Bioconductor
- (2015) Wolfgang Huber et al. NATURE METHODS
- limma powers differential expression analyses for RNA-sequencing and microarray studies
- (2015) Matthew E. Ritchie et al. NUCLEIC ACIDS RESEARCH
- SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
- (2014) Y. Xie et al. BIOINFORMATICS
- Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
- (2014) Rob Patro et al. NATURE BIOTECHNOLOGY
- rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
- (2014) Shihao Shen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Differential abundance analysis for microbial marker-gene surveys
- (2013) Joseph N Paulson et al. NATURE METHODS
- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
- (2013) Daehwan Kim et al. GENOME BIOLOGY
- Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
- (2012) Marcel H. Schulz et al. BIOINFORMATICS
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- Detecting differential usage of exons from RNA-seq data
- (2012) S. Anders et al. GENOME RESEARCH
- Differential analysis of gene regulation at transcript resolution with RNA-seq
- (2012) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- Streaming fragment assignment for real-time analysis of sequencing experiments
- (2012) Adam Roberts et al. NATURE METHODS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
- (2012) Cole Trapnell et al. Nature Protocols
- The Human Transcriptome: An Unfinished Story
- (2012) Mihaela Pertea Genes
- RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
- (2011) Bo Li et al. BMC BIOINFORMATICS
- IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly
- (2011) Wei Li et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Full-length transcriptome assembly from RNA-Seq data without a reference genome
- (2011) Manfred G Grabherr et al. NATURE BIOTECHNOLOGY
- The sequence read archive: explosive growth of sequencing data
- (2011) Y. Kodama et al. NUCLEIC ACIDS RESEARCH
- Fast and SNP-tolerant detection of complex variants and splicing in short reads
- (2010) T. D. Wu et al. BIOINFORMATICS
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
- (2010) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
- (2010) Mitchell Guttman et al. NATURE BIOTECHNOLOGY
- Analysis and design of RNA sequencing experiments for identifying isoform regulation
- (2010) Yarden Katz et al. NATURE METHODS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
- (2008) Ryan Lister et al. CELL
- Stem cell transcriptome profiling via massive-scale mRNA sequencing
- (2008) Nicole Cloonan et al. NATURE METHODS
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
- (2008) Ali Mortazavi et al. NATURE METHODS
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started