NDLI: An integer programming approach to novel transcript reconstruction from paired-end RNA-Seq reads

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An integer programming approach to novel transcript reconstruction from paired-end RNA-Seq reads

Content Provider	ACM Digital Library
Author	Brinza, Dumitru Mangul, Serghei Banday, Abdul Rouf Al Seesi, Sahar Caciula, Adrian Kanadia, Rahul
Abstract	Massively parallel whole transcriptome sequencing, commonly referred to as RNA-Seq, has become the technology of choice for performing gene expression profiling. However, reconstruction of full-length novel transcripts from RNA-Seq data remains challenging due to the short read length delivered by most existing sequencing technologies. We propose a novel statistical genome-guided method called "Transcriptome Reconstruction using Integer Programming" (TRIP) that incorporates fragment length distribution into novel transcript reconstruction from paired-end RNA-Seq reads. TRIP creates a splice graph based on aligned RNA-Seq reads and enumerates all maximal paths corresponding to putative transcripts. The problem of selecting true transcripts is formulated as an integer program (IP) which minimizes the set of selected transcripts yielding a good statistical fit between the fragment length distribution (empirically determined during library preparation) and fragment lengths implied by mapped read pairs. Experimental results on both real and synthetic datasets show that TRIP is more accurate than methods ignoring fragment length distribution information. The software is available at: http://www.cs.gsu.edu/serghei/?q=trip.
Starting Page	369
Ending Page	376
Page Count	8
File Format	PDF
ISBN	9781450316705
DOI	10.1145/2382936.2382983
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2012-10-07
Publisher Place	New York
Access Restriction	Subscribed
Content Type	Text
Resource Type	Article

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