Partek ^® Flow ^® accepts custom-made Affymetrix .CEL and Illumina .idat or AVGSignal data generated from Genome Studio files as input. These require an accompanying probe annotation file.
This document describes how to create and import your own custom-microarray annotation files for use in Partek Flow.

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It is advisable to obtain the annotation files for your custom chip directly from Affymetrix. If for some reason this is not possible, probe_tab files can be created as a tab-delimited text file using any text editor.
They must contain the following information in columns:

• Probe id: unique ID of the  probe
• Probe x: Probe X position on the chip
• Probe y: Probe Y position on the chip
• Probe sequence: sequence of the  probe, all IUPAC nucleotide codes are supported

The first line of the file must be the column headings listed abovebelow. Any mixture of upper and lower case is supported. If you are modifying this from another file, the Probe Id column must be the first column in the file. The order of the other columns does not matter and any additional columns will be ignored unless they are in conflict with the column names above.

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Remember to save your modified file with a .probe_tab extension.

Note: Below is the preferred column header example: Probe_id    Probe_x    Probe_y    Probe_sequence

Creating Custom Illumina Annotation Files

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Importing Annotation Files into Library File Management

The annotation files can then be uploaded into Partek Flow by going to Settings>Library File Management, selecting the Microarray library files tab and clicking the Add probe sequence button (Figure 1). 

Converting Custom Microarray Files into Aligned Reads

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When prompted to select the probe sequence file, click the Chip name drop-down menu and select the chip name for your custom chip. 

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