Alignment and mapping methodology influence transcript abundance estimation
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Summary
This work investigates the influence of mapping and alignment on the accuracy of transcript quantification in both simulated and experimental data, as well as the effect on subsequent differential expression analysis, and introduces a new alignment methodology to overcome the shortcomings of lightweight approaches without incurring the computational cost of traditional alignment.
- Type
- preprint
- Published
- 2019-06-03
- Cited by
- 161
- References
- 62
- Access
- Open access
- OpenAlex
- https://openalex.org/W2948240282
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:195435380
Keywords
Computer science, Data mining, Expression (computer science), Differential (mechanical device), Artificial intelligence
References
- Widespread disruption of host transcription termination in HSV-1 infection
- Fast and accurate approximate inference of transcript expression from RNA-seq data
- The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
- RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
- Cutadapt removes adapter sequences from high-throughput sequencing reads
- Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
- Highly integrated single-base resolution maps of the epigenome in Arabidopsis.
- RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations
- DNA sequence of mutations induced in cells by herpes simplex virus type-1.
- Identifying differentially expressed transcripts from RNA-seq data with biological variation
- Errors in RNA-Seq quantification affect genes of relevance to human disease
- Pathways Disrupted in Human ALS Motor Neurons Identified Through Genetic Correction of Mutant SOD1
- Polyester: Simulating RNA-Seq Datasets With Differential Transcript Expression
- RNA-Skim: a rapid method for RNA-Seq quantification at transcript level
- Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
- voom: precision weights unlock linear model analysis tools for RNA-seq read counts
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
- Fast gapped-read alignment with Bowtie 2
- Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
- Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
Cited by
- Transcriptomic and evolutionary analysis of the mechanisms by which P. argentatum, a rubber producing perennial, responds to drought
- Exploring Lossy Compression of Gene Expression Matrices
- Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data
- Technology dictates algorithms: recent developments in read alignment
- pyrpipe: a Python package for RNA-Seq workflows
- Preprocessing choices affect RNA velocity results for droplet scRNA-seq data
- Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis
- Scalable Pairwise Whole-Genome Homology Mapping of Long Genomes with BubbZ
- Puffaligner: An Efficient and Accurate Aligner Based on the Pufferfish Index
- Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny
- PISCES: a package for rapid quantitation and quality control of large scale mRNA-seq datasets
- Algorithms and Data Structures for Indexing, Querying, and Analyzing Large Collections of sequencing Data in the presence or Absence of a Reference
- Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq
- Benchmarking of lightweight-mapping based single-cell RNA-seq pre-processing
- noisyR: Enhancing biological signal in sequencing datasets by characterising random technical noise
- Accounting for fragments of unexpected origin improves transcript quantification in RNA-seq simulations focused on increased realism
- A like-for-like comparison of lightweight-mapping pipelines for single-cell RNA-seq data pre-processing
- Comparative analysis of common alignment tools for single-cell RNA sequencing
- Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines
- Transplanted Erythropoietin-Expressing Mesenchymal Stem Cells Promote Pro-survival Gene Expression and Protect Photoreceptors From Sodium Iodate-Induced Cytotoxicity in a Retinal Degeneration Model
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