An existing ChIPMonk project can be opened by selecting File > Open. As well as loading the project data this will also load the correct genome (or download it if you don't currently have it).
When you've finished working on your project you can save it 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.
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.
To begin to create a new project select File > New Project from the main menu. You will be provided with a tree view of the genomes you currntly have available. These will be classified firstly by species and then by assembly.
It is important that you select the correct genome assembly for the array you are going to use. Selecting the wrong array will result in probes being positioned incorrectly on the genome, or possibly not appearing at all.
There is no universal rule for how to determine which assembly to use, if you are unsure which genome to use you should ask the producer of your array for this information.
Once you have selected the correct genome it will be loaded into ChipMonk. This may take a minute or so since there's a lot of information in a genome! Once the genome has loaded you are ready to import your data.
If the genome you require does not appear in the list of available genomes you will need to download and install it into ChIP Monk. Because of the size of the genome annotation files it is not practical to ship a large number of these with the program.
Importing a new genome is a fairly straightforward process. After selecting File > New Project press the button which says "Import New" ChIPMonk will fetch a list of genomes from our website and give you a selectable tree to choose the one you want to import. Select the genome you want and press "Download". The genome will be downloaded and installed in your genomes folder. You can then use it to create a new project.
If you want to use a genome which isn't available on the download server then please report this as a bug (www.bioinformatics.bbsrc.ac.uk/bugzilla/) and we can add more genomes to the system. If you want to make up your own genome files then this is also fairly straightforward to do (they're just EMBL header files). Please contact the authors and we'll give you the details of how to do this.
Once your genome has loaded you can begin to import data. The data import process will be slightly different for different array formats. To begin to import data simply select File > Import and then pick the correct format for your array.
The data file you need to import your Nimblegen data into ChIP Monk can be found in the Pair Files folder of your Nimblegen DVD and is called all_pair.txt.
ChIP Monk will be able to extract the sample names from the all_pair.txt file, but it won't know which pairs of data go together, and which experimental condition each represents.
After selecting the data file you wish to use you will be presented with a dialog box which you should use to pair up your data sets. Each pair consists of a total DNA control sample, and an experimental DNA subset. Select one data set in each column and press "Make new sample". You will be asked for a sample name for each pair.
When you've added all the pairs you want press the "Done" button to begin to import the data. You don't have to use all of the data sets in a data file. The data will then be imported and you can begin your analysis.
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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