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Old 01-17-2013, 07:44 PM   #43
Location: Melbourne (Victoria) Australia

Join Date: Sep 2011
Posts: 30

Hi Valeu,

This is Fernando again. I have re-run Freec on one of my samples where I previously run CNA analysis from a SAM file (unsorted, I use the FR mateOrientation parameter). The difference this time was that I wanted to run CNA + BAF analyses. To run BAF I first created a pileup from the sample SAM file and then run it using exactly the same parameters.
Even though that the results look graphically the same (R created plots), when I compared the CNVs text files produced by both analyses the results look slightly different. The differences are seen in the start and end position (the regions are roughfly the same) and in terms the copy number predicted.
Are there any reasons why this could be happening? Which one should be more reliable?
Thanks in advance.



Last edited by fjrossello; 01-17-2013 at 07:45 PM. Reason: typo
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