Hello!
I have successfully run the oncoanalyser pipeline, but I can’t find (or understand) information per gene of copy number alteration. I’m interested in all genes, not only driver ones.
Thanks and sorry if its a naive question.
Marcel
It should be in the purple results subdirectory, in a file with the extension purple.cnv.gene.tsv , and in case you want them the segment values are found in the .cnv.somatic.tsv.
In the per-gene file, my interpretation is that the column for total copy number is (effectively) maxCopyNumber.
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maxCopyNumber refers to the maximum copy number in that gene body, and likewise for minCopyNumber, in case there are copy number breakpoints inside the gene body. Most of the time they are the same number.
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Thanks both of you!
Yes, in my data they ususually have the same values and I understand why.
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