Question: ABSOLUTE output interpretation
0
gravatar for 9521ljh
17 months ago by
9521ljh20
9521ljh20 wrote:

i have two bam file (normal.bam and tumor.bam )

i run CNVkit(tool) to find out copy number. After i ran i have get to know tumor purity and ploidy are important factor to uncover Copy number.

Thus, i find the tool for identify purity and ploidy, "ABSOLUTE", and ran it.

But i can't find the document of interpretation of output.

enter image description here

  1. In this plot i don't know the dot means
  2. Which one is representative purity of tumor(y-axis) ?????
ploidy purity absolute scna • 803 views
ADD COMMENTlink modified 17 months ago by Kevin Blighe66k • written 17 months ago by 9521ljh20
0
gravatar for Kevin Blighe
17 months ago by
Kevin Blighe66k
Kevin Blighe66k wrote:

There is an explanation of the plot, here: http://software.broadinstitute.org/cancer/software/genepattern/analyzing-absolute-data

a

It just shows how, given any copy number profile, there are going to be more than just one model that explain the copy number profile when considering purity (y-axis) and ploidy (x-axis).

Kevin

ADD COMMENTlink written 17 months ago by Kevin Blighe66k
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