This is the code used to run the RNAseq analysis for the her3 knockout in zebrafish. The easiest way to view the analysis is to look at kentRNAseq1.html in a browser. This code is meant not as a plug-and-play pipeline for running RNAseq analysis, but rather to document the steps involved in running this analysis.
The code to run this analysis can be found in kentRNAseq1.Rmd. It may be easier to view the code by downloading kentRNAseq1.html and viewing it in a browser.
All sbatch commands used in the analysis are in the sbatchCmds folder and any code for other scripts are viewable in the source code blocks of the html file.
If you have questions on the study, please contact Matt Kent or Genevieve Kendall.