Systematic evaluation of spliced alignment programs for RNA-seq data
| العنوان: | Systematic evaluation of spliced alignment programs for RNA-seq data |
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| المؤلفون: | Engström, Pg, Steijger, T, Sipos, B, Grant, Gr, Kahles, A, Alioto, T, Behr, J, Bertone, P, Bohnert, R, Campagna, Davide, Davis, Ca, Dobin, A, Gingeras, Tr, Goldman, N, Guigó, R, Harrow, J, Hubbard, Tj, Jean, G, Kosarev, P, Li, S, Liu, J, Mason, Ce, Molodtsov, V, Ning, Z, Ponstingl, H, Prins, Jf, Rätsch, G, Ribeca, P, Seledtsov, I, Solovyev, V, Valle, Giorgio, Vitulo, Nicola, Wang, K, Wu, Td, Zeller, G, Rgasp, Consortium |
| المساهمون: | Laboratoire d'Informatique de Nantes Atlantique (LINA), Centre National de la Recherche Scientifique (CNRS)-Mines Nantes (Mines Nantes)-Université de Nantes (UN), The Wellcome Trust Sanger Institute [Cambridge], Centro de Regulación Genómica (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Department of Computer Science [Royal Holloway], Royal Holloway [University of London] (RHUL), CRIBI (CRIBI), Universita degli Studi di Padova, Dipartimento di Scienze, Tecnologie e Mercati della Vite e del Vino, University of Verona (UNIVR), Sanger Institute, Wellcome Trust, Bertone, Paul [0000-0001-5059-4829], Apollo - University of Cambridge Repository |
| المصدر: | Nature methods Nature Methods Nature Methods, Nature Publishing Group, 2013, epub ahead of print. ⟨10.1038/nmeth.2722⟩ Recercat. Dipósit de la Recerca de Catalunya instname |
| سنة النشر: | 2013 |
| مصطلحات موضوعية: | False discovery rate, Sequence analysis, RNA Splicing, Messenger, Animals, Chromosome Mapping, Computational Biology, Exons, False Positive Reactions, High-Throughput Nucleotide Sequencing, Humans, K562 Cells, Mice, RNA, Messenger, Reproducibility of Results, Sequence Alignment, Sequence Analysis, RNA, Software, RNA-Seq, Sequence alignment, Computational biology, Biology, Biochemistry, Article, 03 medical and health sciences, Exon, 0302 clinical medicine, Empalmament (Genètica), Gens Mapatge, Molecular Biology, 030304 developmental biology, Genetics, 0303 health sciences, business.industry, Cell Biology, Gene Annotation, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 030220 oncology & carcinogenesis, RNA splicing, RNA, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, Sequence Analysis, Biotechnology |
| الوصف: | LINA-COMBI; International audience; : High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions. |
| وصف الملف: | application/pdf |
| اللغة: | English |
| تدمد: | 1548-7105 1548-7091 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6385fd1559cfdc01d937b50d88596646Test http://europepmc.org/articles/PMC4018468Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....6385fd1559cfdc01d937b50d88596646 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15487105 15487091 |
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