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The Processes Performed

The pregap stages are as follows:

  1. General initialisation

  2. Convert the raw trace file to an SCF file.

  3. Estimate Base Accuracies.

  4. Create experiment files.

  5. Augment the experiment files.
  6. Perform quality clipping (optional).

  7. Perform vector clipping (optional).

  8. Perform interactive quality clipping (optional).

  9. Screen against vector (optional).

  10. Tag repeat segments (optional).

  11. Find mutations (optional)

  12. Sort results (optional)

  13. Final preparations.

[picture]

The flow of data through the pregap stages. The input file formats are shown at the top along with any necessary conversion stages. The dotted arrows show paths to skip the optional stages.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap_2.html