The following files are nessesary to run RATools. In the RATools directory a subdirectory for a particular experiment is created ( e.g. RATools/EXPERIMENT ). This directory contains the unique chip design, primer locations, and images. The following files must be present in that directory for a successful basecall. Note that Experiment and EXPERIMENT can be any user defined contiguous experiment name.

• Filename: Experiment.cdf

  • Location: EXPERIMENT Subdirectory

  • Contents: This contains the description of the chip design.

• Filename: Experiment.primers.txt

  • Location: EXPERIMENT Subdirectory

  • Contents: This file contains the description of the primer locations. It is used downstream to detect primer failure and omit certain bases from the sequence call. If PCR was not used to amplify the target DNA a substitute file should be created simply using the start and stop of each sequence on the array.

    1       130
    131     1107
    1108    1854
    1855    56359
    

• Filename: Experiment.genpos.txt

  • Location: EXPERIMENT Subdirectory

  • Contents: The genpos file, exactly the same as the primer file.

• Filename: Experiment.genpos.txt

  • Location: EXPERIMENT Subdirectory

  • Contents: The genpos file is exactly the same as the primer file.

• Filename: *.DAT

  • Location: EXPERIMENT Subdirectory

  • Contents: these contain the raw chip images directly from the scanner.