This pipeline uses an annotated genome to identify differential expressed genes/transcripts. 15 hour minimum ($1320 internal$1470 internal, $1680 $1860 external) per project.
1. Quality Assessment
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- Sample dendogram
- Sample-Sample correlation plot
- Pair plot: Matrix of scatter plots showing relationship of every sample metadata variable to every other variable.
- Expression heatmap with clustering of samples
- Volcano plot : Scatter plot of fold-change versus significance
- Box plots of top 10 upregulated and top 10 downregulated genes.
- PCA plot: Orthogonal transformation of the data to look at underlying structure of data.
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