Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage
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Summary
It is shown that an incomplete annotation catalog can have a detrimental effect on the ability to detect differential transcript usage in transcriptomes with few isoforms per gene and that isoform-level prefiltering can considerably improve false discovery rate control.
- Type
- article
- Published
- 2016-01-26
- Cited by
- 133
- References
- 42
- Access
- Open access
- OpenAlex
- https://openalex.org/W2268486506
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:7324534
Keywords
False discovery rate, Alternative splicing, Annotation, Biology, Inference
References
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- A comparison of methods for differential expression analysis of RNA-seq data
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- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Cited by
- Open Peer Review
- Arkas: Rapid, Reproducible RNAseq Analysis as a Service
- A benchmark for RNA-seq quantification pipelines
- Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq
- DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics
- Robust identification of Ptbp1-dependent splicing events by a junction-centric approach in Xenopus laevis.
- Faithful mRNA splicing depends on the Prp19 complex subunit faint sausage and is required for tracheal branching morphogenesis in Drosophila
- Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells
- A general and powerful stage-wise testing procedure for differential expression and differential transcript usage
- Arkas: Rapid reproducible RNAseq analysis
- SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Identifying differential isoform abundance with RATs: a universal tool and a warning
- Identifying core biological processes distinguishing human eye tissues with systems-level gene expression analyses and weighted correlation networks
- Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries
- Bayesian estimation of differential transcript usage from RNA-seq data
- stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage
- Yanagi: Transcript Segment Library Construction for RNA-Seq Quantification
- Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm
- FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data
- Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7
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