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U. Lopez de Heredia, J.L. Vazquez-Poletti. RNA-seq Analysis in Forest Tree Species: Bioinformatic Problems and Solutions. Tree Genetics & Genomes, 12(2):1-17, 2016.


Direct sequencing of RNA (RNA-seq) using next-generation sequencing platforms has allowed a growing number of gene expression studies focused on forest trees in the last 5 years. Bioinformatic analyses derived from RNA-seq of forest trees are particularly challenging, because the massive genome length ( 20.1 Gbp for loblolly pine) and the absence of annotated reference genomes require specific bioinformatic pipelines to obtain sound biological results. In the present manuscript, we review common bioinformatic challenges that researchers need to consider when analyzing RNA-seq data from forest tree species at the light of the experience acquired from recent studies. Furthermore, we list bioinformatic pipelines and data processing software available to overcome RNA-seq limitations. Finally, we discuss the impact of novel computation solutions, such as the cloud computing paradigm that allows RNA-seq analysis even for small research centers with limited resources


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Jose Luis Vazquez-Poletti

BibTex Reference

   Author = {Lopez de Heredia, U. and Vazquez-Poletti, J.L.},
   Title = {RNA-seq Analysis in Forest Tree Species: Bioinformatic Problems and Solutions},
   Journal = {Tree Genetics & Genomes},
   Volume = {12},
   Number = {2},
   Pages = {1--17},
   Year = {2016}

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