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Fig. 1 | BMC Bioinformatics

Fig. 1

From: VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

Fig. 1

Overview of the full workflow performed by VIPER (Visualization Pipeline for RNAseq analysis). The different segments of the pipeline are broken down by color. The core of the pipeline is the read alignment performed by STAR that outputs alignment (bam) files. Gene expression is quantitated with Cufflinks for unsupervised analysis (clustering and PCA). STAR also generates a count matrix used for supervised analysis (differential expression with DESeq2). When a publically available analysis tool is used for a particular step, the name of the tool is identified above the arrow leading to the resulting output (boxed). When there is no tool indicated next to an arrow, the analysis step was performed with custom R code. Conditional/optional analyses are denoted with a hashed arrow and outlining box and represent the most distinguishing functionality for VIPER

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