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TRIP: A method for novel transcript reconstruction from paired-end RNA-seq reads
Mangul, Serghei Caciula, Adrian Brinza, Dumitru Măndoiu, Ion I Zelikovskiy, Alexander
Mangul, Serghei
Caciula, Adrian
Brinza, Dumitru
Măndoiu, Ion I
Zelikovskiy, Alexander
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Abstract
Preliminary experimental results on synthetic datasets generated with various sequencing parameters and distribution assumptions show that TRIP has increased transcriptome reconstruction accuracy compared to previous methods that ignore fragment length distribution information.
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This article was originally published in BMC Bioinformatics.
© 2012 Mangul et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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2012-01-01
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Keywords
DNA sequencing, massively parallel sequencing, RNA-Seq, transcriptome research, transcriptome analyses, genome-guided method, Transcriptome Reconstruction using Integer Programing (TRIP), directed acyclic graph (DAG), depth-first-search (DFS) algorithm, transcriptome reconstruction
Citation
Mangul et al.: TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads. BMC Bioinformatics 2012 13(Suppl 18):A11. doi: 10.1186/1471-2105-13-S18-A11