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Similar to previously described steps, first time users will be asked to create the Marker file. Partek Flow does not currently host any marker files, however, users may add them as library files. Marker files should be a .txt file with the marker information in correct format. The same example in the Garnett tutorial of a simple valid Marker file is provided here (Figure 5).  Note that there has to be a space character after the colon and that there has to be a space characher after the comma.

Note:

1) Cell type name line starts with ">", followed by the name of the cell type.

2) Definition line starts with a keyword e.g. "expressed", "not expressed" eg. it is case sensitive. It followed by a ":" and space. Each gene name is followed by a comma and space. The line cannot be ended with comma and space.

For more details on how to construct a Marker file, please refer to Garnett tutorial³. Next, click the Create button and Partek Flow will then save the file with the name that users provide for future use (Figure 6a).

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