In order to use Caryoscope, your data must be in one of the following formats:
The General Feature Format (Version 2) (see Section 3.4.1, “General Feature Format”); or
A spreadsheet-compatible text format (i.e., comma or tab separated) (see Section 3.4.2, “Spreadsheet-compatible text”).
In this tutorial, we assume that you are obtaining your data from the Stanford Microarray Database (SMD). The SMD software provides utilities to perform a "genome alignment" of your experiment data, and always produces a file that is compatible with Caryoscope. This file will typically be named *.gff (if it is a GFF file) or *.csv or *.txt (if it is a comma or tab delimited spreadsheet-compatible text file, respectively).
See Section 3.7, “Integrating with the Stanford Microarray Database” for more information about using Caryoscope with data from the Stanford Microarray Database.