ArticleGenome biology2013
CRAC: an integrated approach to the analysis of RNA-seq reads.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- A Versatile Ribo-seq Workflow for Enhanced Analysis of Ribosome Dynamics.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data.Genome biology · 2024Article
- Limited contribution of the of P2X4 receptor to LPS-induced microglial reaction in mice.Purinergic signalling · 2024Article
- Effective requesting method to detect fusion transcripts in chronic myelomonocytic leukemia RNA-seq.NAR genomics and bioinformatics · 2024Article
- Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model.PLoS computational biology · 2023Article
- Alternative splicing analysis benchmark with DICAST.NAR genomics and bioinformatics · 2023Article
- Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r.BMC bioinformatics · 2022Article
- Kmerator Suite: design of specificNAR genomics and bioinformatics · 2021Article
- Technology dictates algorithms: recent developments in read alignment.Genome biology · 2021Review
- Long non-coding RNA exploration for mesenchymal stem cell characterisation.BMC genomics · 2021Article
- Comparative Genome-Wide Transcriptome Analysis ofFrontiers in microbiology · 2021Article
- Evidence of constraint in the 3D genome for trans-splicing in human cells.Science China. Life sciences · 2020Article
- Zooming in on protein-RNA interactions: a multi-level workflow to identify interaction partners.Biochemical Society transactions · 2020Review
- Molecular entrapment by RNA: an emerging tool for disrupting protein-RNA interactionsRNA biology · 2020Article
- Interpretation of differential gene expression results of RNA-seq data: review and integration.Briefings in bioinformatics · 2019Review
- RNA-protein interactions: disorder, moonlighting and junk contribute to eukaryotic complexity.Open biology · 2019Review
- Unravelling paralogous gene expression dynamics during three-spined stickleback embryogenesis.Scientific reports · 2019Article
- Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Exploiting non-canonical translation to identify new targets for T cell-based cancer immunotherapy.Cellular and molecular life sciences : CMLS · 2018Review
- A New Machine Learning-Based Framework for Mapping Uncertainty Analysis in RNA-Seq Read Alignment and Gene Expression Estimation.Frontiers in genetics · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A large number of RNA-sequencing studies set out to predict mutations, splice junctions or fusion RNAs. We propose a method, CRAC, that integrates genomic locations and local coverage to enable such predictions to be made directly from RNA-seq read analysis. A k-mer profiling approach detects candidate mutations, indels and splice or chimeric junctions in each single read. CRAC increases precision compared with existing tools, reaching 99:5% for splice junctions, without losing sensitivity. Importantly, CRAC predictions improve with read length. In cancer libraries, CRAC recovered 74% of validated fusion RNAs and predicted novel recurrent chimeric junctions. CRAC is available at http://crac.gforge.inria.fr.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.