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NimbleGen Data Summary Files

3.11 NimbleGen Data Summary Files

The NimbleGen data summary file import tool reads NimbleGen *_segMNT.txt text files (TXT tab delimited files) that were created using Roche NimbleGen Software and allows you to import various log ratio fields into SVS for analysis. The selected field is imported into SVS and a marker map is created and applied to the dataset.

From the Import NimbleGen Data dialog (see Figure 17), first select the TXT files you want to include in the dataset. To select the files, click on the Add Files button and use the file browser to choose files for import. The files you selected will appear in the import dialog window. You may add all of the TXT files in a directory by using the Add Directory button. To remove files from the window, select the unwanted samples and click Remove. You may continue adding files by clicking on the Add Files or the Add Directory buttons again. Multiple selection is allowed by <Shift>-left-click to select a block of files or by <Ctrl>-left-click to select several individual files. All TXT files must be of the same type, length and containing the same marker map information in order to be imported together. If there are files that do not match then an error message will be generated and the non-matching files will need to be removed from the list of files to import.

The possible log ratio fields that can be imported one or more at a time (if they are available in all of the text files are:

• LogR Ratio
• LogR Ratio Spatial
• LogR Ratio Corrected

If multiple log ratio data fields are selected, a single dataset will be created for field.

You can also change the name of the dataset at this time.