7. Extracting differentially expressed genes with edgeR

Run this edgeR script (nema.salmon.R) that loads all this. For more information, see the edgeR manual

curl -O -L https://raw.githubusercontent.com/dib-lab/eel-pond/DE/nema.salmon.R
Rscript nema.salmon.R

These will produce two plots, nema-edgeR-MDS.pdf and nema-edgeR-MA-plot.pdf.

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You can see the plot outputs for the whole data set (all the reads) here:

• nema-edgeR-MDS.pdf
• nema-edgeR-MA-plot.pdf (0 vs 6 hour)

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