期刊
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
卷 18, 期 -, 页码 1569-1576出版社
ELSEVIER
DOI: 10.1016/j.csbj.2020.06.014
关键词
RNA-seq; Multi-mapped reads; Duplicated genes; Noncoding RNAs; Gene isoforms; Expectation-maximization algorithm
资金
- Natural Science and Engineering Research Council of Canada [NSERC] [RGPIN-2018-05412]
- Alexander-Graham-Bell Doctoral scholarship from NSERC
- NSERC Masters scholarship
- Fonds de Recherche du Quebec - Sante (FRQS) Research Scholar Junior 2 Career Award
Many eukaryotic genomes harbour large numbers of duplicated sequences, of diverse biotypes, resulting from several mechanisms including recombination, whole genome duplication and retro-transposition. Such repeated sequences complicate gene/transcript quantification during RNA-seq analysis due to reads mapping to more than one locus, sometimes involving genes embedded in other genes. Genes of different biotypes have dissimilar levels of sequence duplication, with long-noncoding RNAs and messenger RNAs sharing less sequence similarity to other genes than biotypes encoding shorter RNAs. Many strategies have been elaborated to handle these multi-mapped reads, resulting in increased accuracy in gene/transcript quantification, although separate tools are typically used to estimate the abundance of short and long genes due to their dissimilar characteristics. This review discusses the mechanisms leading to sequence duplication, the biotypes affected, the computational strategies employed to deal with multi-mapped reads and the challenges that still remain to be overcome. (C) 2020 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
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