RNA-Seq workflow: gene-level exploratory analysis and differential expression.
RNA-Seq workflow: gene-level exploratory analysis and differential expression.
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RNA-Seq工作流程：基因级探索性分析和差异表达。
DOI：
10.12688/f1000research.7035.1
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发表时间：
2015
期刊：
影响因子：
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通讯作者：
Huber W
中科院分区：
文献类型：
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作者：
Love MI;Anders S;Kim V;Huber W
在这里，我们使用BioConductor软件包介绍了端到端基因级别的RNA-Seq差异表达工作流程。我们将从FASTQ文件开始，展示这些文件是如何与参考基因组比对的，并准备一个计数矩阵，其中包括每个样本每个基因内的RNA-seq读数/片段数。我们将进行探索性数据分析(EDA)以进行质量评估和分析，以探索样本之间的关系，执行差异基因表达和分析，并直观地探索结果。
Here we walk through an end-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results.