ArticleBioinformatics (Oxford, England)2017
Rail-RNA: scalable analysis of RNA-seq splicing and coverage.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
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- Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models.Nature biotechnology · 2023Article
- A Drug Repurposing Pipeline Based on Bladder Cancer Integrated Proteotranscriptomics Signatures.Methods in molecular biology (Clifton, N.J.) · 2023Article
- RNA-seq data science: From raw data to effective interpretation.Frontiers in genetics · 2023Review
- SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses.Genomics, proteomics & bioinformatics · 2022Article
- OMiCC: An expanded and enhanced platform for meta-analysis of public gene expression data.STAR protocols · 2022Article
- Empirical prediction of variant-activated cryptic splice donors using population-based RNA-Seq data.Nature communications · 2022Article
- recount3: summaries and queries for large-scale RNA-seq expression and splicing.Genome biology · 2021Article
- Targeting Tumor-Stromal IL6/STAT3 Signaling through IL1 Receptor Inhibition in Pancreatic Cancer.Molecular cancer therapeutics · 2021Article
- Bias-invariant RNA-sequencing metadata annotation.GigaScience · 2021Article
- Single cell derived mRNA signals across human kidney tumors.Nature communications · 2021Article
- SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.BMC bioinformatics · 2021Article
- GPrimer: a fast GPU-based pipeline for primer design for qPCR experiments.BMC bioinformatics · 2021Article
- A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways.PLoS computational biology · 2021Article
- Methods for correcting inference based on outcomes predicted by machine learning.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Epigenomic and Transcriptomic Dynamics During Human Heart Organogenesis.Circulation research · 2020Article
- BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis.Bioinformatics (Oxford, England) · 2020Article
- Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival.Genome medicine · 2020Article
- Putatively cancer-specific exon-exon junctions are shared across patients and present in developmental and other non-cancer cells.NAR cancer · 2020Article
- Variability in estimated gene expression among commonly used RNA-seq pipelines.Scientific reports · 2020Article
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Authors and funding
9 authors.
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Abstract
motivationRNA sequencing (RNA-seq) experiments now span hundreds to thousands of samples. Current spliced alignment software is designed to analyze each sample separately. Consequently, no information is gained from analyzing multiple samples together, and it requires extra work to obtain analysis products that incorporate data from across samples.
resultsWe describe Rail-RNA, a cloud-enabled spliced aligner that analyzes many samples at once. Rail-RNA eliminates redundant work across samples, making it more efficient as samples are added. For many samples, Rail-RNA is more accurate than annotation-assisted aligners. We use Rail-RNA to align 667 RNA-seq samples from the GEUVADIS project on Amazon Web Services in under 16 h for US$0.91 per sample. Rail-RNA outputs alignments in SAM/BAM format; but it also outputs (i) base-level coverage bigWigs for each sample; (ii) coverage bigWigs encoding normalized mean and median coverages at each base across samples analyzed; and (iii) exon-exon splice junctions and indels (features) in columnar formats that juxtapose coverages in samples in which a given feature is found. Supplementary outputs are ready for use with downstream packages for reproducible statistical analysis. We use Rail-RNA to identify expressed regions in the GEUVADIS samples and show that both annotated and unannotated (novel) expressed regions exhibit consistent patterns of variation across populations and with respect to known confounding variables. AVAILABILITY AND IMPLEMENTATION: Rail-RNA is open-source software available at http://rail.bio. CONTACTS: anellore@gmail.com or langmea@cs.jhu.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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.