This repository contains all scripts and data used in the lab to perform RNAseq, ATACseq, and ChIPseq data analysis.
Create in your computer a folder for your specific project, this folder must contain the following subfolders:
- data -> it will contain all your raw data to be used for the analysis
- doc -> documentation useful for the project (papers, manuals...)
- figs -> where all the figures rendered over the analysis will be generated
- output -> tables and matrixs generated from the analysis in txt or excel format
- R -> it contains the script(s) used for the specific analysis
Each project will be in a different folder. In the folder you will find a README that explains all you need to perform that specific analysis, including necessary data, documentation, how to use the script, output files and figs, etc.
- After you created your directory in your computer, download data and script(s) following instructions in the README and put them in the corresponding subfolders of your project.
- To run the scripts, always first revisit parameters that need to be changed for each analysis (e.g. directory, input files, conditions, etc.).
- Each project will contain also an MD file in case you want to run the analysis and get a single pdf report with all the figures and tables.