Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Nature Protocols

• Publication date

  2016-08-11

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1038/nprot.2016.095PMID 27560171PMCID PMC5032908
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

  2015cited by this paper
• limma powers differential expression analyses for RNA-sequencing and microarray studies

  2015cited by this paper
• HISAT: a fast spliced aligner with low memory requirements

  2015cited by this paper
• Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

  2015cited by this paper
• Orchestrating high-throughput genomic analysis with Bioconductor

  2015cited by this paper
• Errors in RNA-Seq quantification affect genes of relevance to human disease

  2015cited by this paper
• Ballgown bridges the gap between transcriptome assembly and expression analysis

  2015cited by this paper
• rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

  2014cited by this paper
• Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

  2014cited by this paper
• Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms

  2013cited by this paper
• STAR: ultrafast universal RNA-seq aligner

  2013cited by this paper
• TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

  2013cited by this paper
• Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

  2013cited by this paper
• SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

  2013cited by this paper
• Robust methods for differential abundance analysis in marker gene surveys

  2013cited by this paper
• Streaming fragment assignment for real-time analysis of sequencing experiments

  2012cited by this paper
• Differential analysis of gene regulation at transcript resolution with RNA-seq

  2012cited by this paper
• Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

  2012cited by this paper
• Fast gapped-read alignment with Bowtie 2

  2012cited by this paper
• Detecting differential usage of exons from RNA-seq data

  2012cited by this paper
• Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

  2012cited by this paper
• The Human Transcriptome: An Unfinished Story

  2012cited by this paper
• Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data

  2011cited by this paper
• IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly

  2011cited by this paper
• The sequence read archive: explosive growth of sequencing data

  2011cited by this paper
• RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

  2011cited by this paper
• Fast and SNP-tolerant detection of complex variants and splicing in short reads

  2010cited by this paper
• Corrigendum: Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

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