ArticleNucleic acids research2016
The exon quantification pipeline (EQP): a comprehensive approach to the quantification of gene, exon and junction expression from RNA-seq data.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- An orally available, brain penetrant, small molecule lowers huntingtin levels by enhancing pseudoexon inclusion.Nature communications · 2022Trial
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- The transcription factor ZNF469 regulates collagen production in liver fibrosis.bioRxiv : the preprint server for biology · 2024Article
- Molecular characterization of chronic cutaneous wounds reveals subregion- and wound type-specific differential gene expression.International wound journal · 2024Article
- Transcriptional profiling of hepatocytes infected with the replicative form of the malaria parasite Plasmodium cynomolgi.Malaria journal · 2022Article
- STING regulates peripheral nerve regeneration and colony stimulating factor 1 receptor (CSF1R) processing in microglia.iScience · 2021Article
- CYP27A1-dependent anti-melanoma activity of limonoid natural products targets mitochondrial metabolism.Cell chemical biology · 2021Article
- Single-cell and bulk transcriptomics of the liver reveals potential targets of NASH with fibrosis.Scientific reports · 2021Article
- CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data.Genome biology · 2019Article
- Transcriptomic analysis reveals reduced transcriptional activity in the malaria parasiteeLife · 2018Article
- TRRAP is a central regulator of human multiciliated cell formation.The Journal of cell biology · 2018Article
- Genome-wide CRISPR screen for PARKIN regulators reveals transcriptional repression as a determinant of mitophagy.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Article
- Profiling RNA-Seq at multiple resolutions markedly increases the number of causal eQTLs in autoimmune disease.PLoS genetics · 2017Article
- A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples.BMC genomics · 2017Article
- Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening.BMC genomics · 2016Article
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Abstract
The quantification of transcriptomic features is the basis of the analysis of RNA-seq data. We present an integrated alignment workflow and a simple counting-based approach to derive estimates for gene, exon and exon-exon junction expression. In contrast to previous counting-based approaches, EQP takes into account only reads whose alignment pattern agrees with the splicing pattern of the features of interest. This leads to improved gene expression estimates as well as to the generation of exon counts that allow disambiguating reads between overlapping exons. Unlike other methods that quantify skipped introns, EQP offers a novel way to compute junction counts based on the agreement of the read alignments with the exons on both sides of the junction, thus providing a uniformly derived set of counts. We evaluated the performance of EQP on both simulated and real Illumina RNA-seq data and compared it with other quantification tools. Our results suggest that EQP provides superior gene expression estimates and we illustrate the advantages of EQP's exon and junction counts. The provision of uniformly derived high-quality counts makes EQP an ideal quantification tool for differential expression and differential splicing studies. EQP is freely available for download at https://github.com/Novartis/EQP-cluster.
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