GISTIC for tetraploid genomes
Hi everyone,
I have a cohort of breast cancer samples and majority of them seems to be unstable and tetraploid.
For GISTIC segFile input, it is mentioned that the copy number should be in this format:
Seg.CN = log2(tumor_copy_number/2)
I am wondering now that my samples are not diploid, should I replace the 2 in denominator by 4 or does GISTIC handle it by itself?
Thanks!
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I'd recommend to run it once to figure out. I'd bet you'll see a "duplicated" sample on the output plot.
In general, GISTIC is very smart and does a lot of work by itself, but in this case I'd just try it on e.g. 30 samples, including tetraploid ones.
Hi, it seems like you've posted this question to GISTIC forum at the same time you posted it here. This practice is frowned upon as you're basically asking two different groups of volunteers (members of which overlap quite a bit) to invest time in your problem. Please do not do this. For GISTIC related questions, their forum is the better place to ask as it is a bit of an esoteric piece of software that is not very well understood IMO.