2024-03-28T22:54:13Zhttp://repisalud.isciii.es/oai/requestoai:repisalud.isciii.es:20.500.12105/75282023-10-13T08:32:08Zcom_20.500.12105_2152com_20.500.12105_2051com_20.500.12105_2144com_20.500.12105_2145col_20.500.12105_2153col_20.500.12105_2146
Repisalud
author
Gatto, Alberto
author
Torroja, Carlos
author
Mazzarotto, Francesco
author
Cook, Stuart A
author
Barton, Paul J R
author
Sanchez-Cabo, Fatima
author
Lara-Pezzi, Enrique
funder
Unión Europea. Comisión Europea
funder
Unión Europea. Comisión Europea. European Research Council (ERC)
funder
Ministerio de Ciencia e Innovación (España)
funder
Comunidad de Madrid (España)
funder
Ministerio de Economía y Competitividad (España)
funder
Fundación ProCNIC
funder
National Health Service (Reino Unido)
2019-04-29T10:17:03Z
2019-04-29T10:17:03Z
2014-04
Nucleic Acids Res. 2014; 42(8):e71
1362-4962
http://hdl.handle.net/20.500.12105/7528
24574529
10.1093/nar/gku166
1362-4962
Nucleic acids research
Alternative splicing is the main mechanism governing protein diversity. The recent developments in RNA-Seq technology have enabled the study of the global impact and regulation of this biological process. However, the lack of standardized protocols constitutes a major bottleneck in the analysis of alternative splicing. This is particularly important for the identification of exon-exon junctions, which is a critical step in any analysis workflow. Here we performed a systematic benchmarking of alignment tools to dissect the impact of design and method on the mapping, detection and quantification of splice junctions from multi-exon reads. Accordingly, we devised a novel pipeline based on TopHat2 combined with a splice junction detection algorithm, which we have named FineSplice. FineSplice allows effective elimination of spurious junction hits arising from artefactual alignments, achieving up to 99% precision in both real and simulated data sets and yielding superior F1 scores under most tested conditions. The proposed strategy conjugates an efficient mapping solution with a semi-supervised anomaly detection scheme to filter out false positives and allows reliable estimation of expressed junctions from the alignment output. Ultimately this provides more accurate information to identify meaningful splicing patterns. FineSplice is freely available at https://sourceforge.net/p/finesplice/.
eng
FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions
journal article
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URL
https://repisalud.isciii.es/bitstream/20.500.12105/7528/1/FineSpliceEnhancedSpliceJunction%20_2014.pdf
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FineSpliceEnhancedSpliceJunction _2014.pdf
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FineSpliceEnhancedSpliceJunction _2014_suppl.pdf
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FineSpliceEnhancedSpliceJunction _2014.pdf.txt
URL
https://repisalud.isciii.es/bitstream/20.500.12105/7528/6/FineSpliceEnhancedSpliceJunction%20_2014_suppl.pdf.txt
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FineSpliceEnhancedSpliceJunction _2014_suppl.pdf.txt