SMART-RDA: A Galaxy Workflow for RNA-Seq Data Analysis
Abstract
RNA-seq using the Next Generation Sequencing (NGS) approach is a common technology to analyze large-scale RNA transcript data for gene expression studies. However, an appropriate bioinformatics tool is needed to analyze a large amount of transcriptomes data from RNA-seq experiment. The aim of this study was to construct a system that can be easily applied to analyze RNA-seq data. RNA-seq analysis tool as SMART-RDA was constructed in this study. It is a computational workflow based on Galaxy framework to be used for analyzing RNA-seq raw data into gene expression information. This workflow was adapted from a well-known Tuxedo Protocol for RNA-seq analysis with some modifications. Expression value from each transcriptome was quantitatively stated as Fragments Per Kilobase of exon per Million fragments (FPKM). RNA-seq data of sterile and fertile oil palm (Pisifera) pollens derived from Sequence Read Archive (SRA) NCBI were used to test this workflow in local facility Galaxy server. The results showed that differentially gene expression in pollens might be responsible for sterile and fertile characteristics in palm oil Pisifera.
Keywords: FPKM; Galaxy workflow; Gene expression; RNA sequencing.
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