Project organisation

It is good practice to keep all files for your project in the same project-specific folder. A well-organised folder structure helps you to have a good overview and facilitates access to the files.
For project standardisation and folder creation you can use something like project templates in R or make your own structure. For example, our project for the RNA-seq analysis looks something like this:

microbepore/
├── doc/
    ├── ...
    ├── ...
    └── ...
├── pipeline/
    ├── ...
    ├── ...
    └── ...    
├── Rscripts/
    ├── ...
    ├── ...
    └── ...
├── data/
    ├── ...
    ├── ...
    └── ...
├── microbepore.Rproj/
├── README.Rmd/
└── LICENSE/

One thing that really helps setting up your R session for a better workflow (especially if you are new to working with many data & if you like to work with R) is setting all up in an RStudio project and using the here package that makes it easier to reference folders. A demonstration of the benefits can be found in Jenny Bryan´s GitHub.