If you have an existing ChIPMonk project file (normally a file whose name ends with .cmk) this can be opened by selecting File > Open. As well as loading the project data this will also download the corresponding genome for the project if you don't have it installed already.
ChIPMonk monitors the work you've done on your project and will prompt you to save your changes if you try to exit the program without saving.
You can save the work you've done at any time by selecting File > Save Project. This will save in ChIPMonk's own data format which will remember your samples, normalisation, probe lists and viewing preferences. The default location for loading and saving projects can be changed under Edit > Preferences > Default Save Location.
No changes you make to a project in ChIPMonk are preserved by default. You must explicitly re-save the project to keep the changes you've made.
If you would like to save a snapshot of your current view in the chromosome view then you can do this by selecting File > Export Current View. This will create a PNG format file which is exactly the same size as your current chromosome view window.
You can save probe lists from within either the probe list viewer or the annotated probe report. You can however also import probe lists into the program by selecting File > Import Probe List. The imported file must be a tab delimited text file where the probe names are in the first column. The first line can be a header and will be ignored if it doesn't contain a valid probe name. Other lines will be ignored as comments if they start with #. Probe lists will only import if all of the probes in the list match the currently loaded data set.
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