# Saving a Project

You can choose to save a project at any point. A SeqMonk project file is a single file which saves both your data and many of your display preferences so that you can get back to working on your data very quickly.

Data which is stored in a project file is:

- The positions of all of your reads
- The details of your samples
- The details of your sample groups
- The positions of your probes
- The quantitated value for all probes for all DataStores
- All current probe lists
- The list of currently visible data and annotation tracks
- The current position of the chromosome view
- The current data zoom level
- The current data view (probes+reads, just probes, just reads)
- The current data scale (positive or positive and negative

Some preferences are not stored in the project file and won't be remembered when the program reopens.

- The genome annotation data (this is referenced and will be downloaded from the SeqMonk server if required)
- The size and layout of the panels in the current display (in case you open the file on a different sized screen)

If you have changed any of the details which SeqMonk stores in its project file during your session, when you close the program you will be prompted to re-save the project before exiting.

You should be aware that because SeqMonk has to write out all of the read data when it saves a project that this can take a few minutes to complete if you have several large datasets open.