The README contains information about this project. Here I will describe my analyses, processing steps, or approaches. Most importantly, the README will contain information about this raw data. Describe 1) how the raw data was generated: bulk ATAC, Cut&Tag, and RNA-seq, 2) where it was obtained: Emory uni, and 3) how it can be accessed for others: tbd. This is the perfect place to describe steps that will be carried out on the command line or on a remote cluster.
STILL TO DO:
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Then clone your new repository locally:
git clone https://github.com/raablab/Gracz.sox9.git
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Rename the
GraczSox9.Rprojfile
The Snakefile is like a recipe book that describes the desired output files, the input files used to make them and the instructions for transforming inputs into outputs. Everytime you create an output file of any type, make sure to add it to the Snakefile. This ensures that changes to your scripts will produce the most up-to-date outputs after running snakemake.
Snakemake comes packaged with the longleaf Anaconda module. Run module load anaconda to access it.
The project template is laid out with the following example structure. Feel free to remove or add as you feel necessary for you project
project-template/
├── data
│ ├── derived_data <- 'Final' analysis outputs, like differential binding/expression tables.
│ │ ├── atac
│ │ ├── cnr
│ │ ├── integrate
│ │ └── rna
│ ├── external <- Location for potential public or non-pipeline processed data
│ ├── processed_data <- Intermediate datasets, like summarizedExperiment RDS files or consensus peak calls
│ │ ├── atac
│ │ ├── cnr
│ │ └── rna
│ └── source_data <- Here is where I will link in data from pipeline runs
│ ├── atac
│ ├── cnr
│ └── rna
├── figures <- Any graphical outputs -- boxplots, scatterplots, etc
│ ├── atac
│ ├── cnr
│ ├── integrate
│ └── rna
├── GraczSox9.Rproj <- Rename this to your project name
├── README.md
├── renv
├── renv.lock <- For use with the `renv` package. Helps everyone stay in the same R environment
├── Snakefile <- See above
└── src <- All code necessary to generate figures and derived data
├── atac
│ └── clean_atac.R
├── cnr
│ └── clean_cnr.R
├── create_canonical_sheet.R
├── integrate
│ └── integrate.R
└── rna
└── clean_rna.R