Publication: SISTEMA DE PROCESAMIENTO Y VISUALIZACIÓN DE DATOS GENÓMICOS PARA LA PRODUCCIÓN DE UVA
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Date
2018-10
Authors
GALAZ VILLARROEL, CLAUDIO ESTEBAN
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Abstract
Chile es uno de los países con mayor producción de uva a nivel mundial, ya sea como fruta de mesa o para la elaboración de vino. Para generar un producto de calidad se hace importante supervisar todo el crecimiento de la vid, además de cosechar la fruta en el momento indicado. Actualmente, el desarrollo de la planta es controlado de manera visual, pero la disminución en costos de la secuenciación de ARN (RNA-Seq) motivan otro acercamiento a esta problemática. En este trabajo se utilizan datos de Vitis vinifera ya existentes, provenientes de ArrayExpress, para generar un pipeline RNA-Seq rápido que incluya el análisis de expresión génica de las etapas fenológicas de la planta. Se utiliza un flujo de trabajo que considera las herramientas FastQC, Trimmomatic, Salmon, edgeR y PANTHER DB. Además se genera el prototipo para una plataforma de visualización, utilizando Shiny, que muestra un resumen del análisis RNA-Seq realizado. El prototipo se encuentra disponible en https://vitis-deg.shinyapps.io/shiny-app/.
Chile is one of the top producers of grape worldwide, either as table fruit or winemaking. To elaborate a quality product it is important to monitor the whole grapevine growth process, in addition to harvesting the fruit at the exact time. Currently, the grapevine development is controlled visually, but the decrease in RNA sequencing costs motivates another approach to this problem. In this work, existing data for Vitis vinifera is used, provenient from ArrayExpress, to generate a fast RNA-Seq pipeline that includes gene expression analysis for phenologic stages of the grapevine. The tools used in the workflow are FastQC, Trimmomatic, Salmon, edgeR and PANTHER DB. Also, a Shiny-based prototype for a visualization platform is presented, with a summary for RNA-Seq results. The prototype is available in https://vitis-deg.shinyapps.io/shiny-app/.
Chile is one of the top producers of grape worldwide, either as table fruit or winemaking. To elaborate a quality product it is important to monitor the whole grapevine growth process, in addition to harvesting the fruit at the exact time. Currently, the grapevine development is controlled visually, but the decrease in RNA sequencing costs motivates another approach to this problem. In this work, existing data for Vitis vinifera is used, provenient from ArrayExpress, to generate a fast RNA-Seq pipeline that includes gene expression analysis for phenologic stages of the grapevine. The tools used in the workflow are FastQC, Trimmomatic, Salmon, edgeR and PANTHER DB. Also, a Shiny-based prototype for a visualization platform is presented, with a summary for RNA-Seq results. The prototype is available in https://vitis-deg.shinyapps.io/shiny-app/.
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Keywords
PROCESAMIENTO DE DATOS , ADMINISTRACION DE LA PRODUCCION , BIOINFORMATICA , GENOMICA