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kunstner / freec2gistic

Workflow: Convert CONTROL-freec output to GISTIC2
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questions #2

Open dodoflyy opened 2 years ago

dodoflyy commented 2 years ago

Hello, I havn't use your script yet. But I have read your code and want to ask 2 questions.
First I see you sum all reads in cpn which overlaps with regions from ratio file, but if you run FREEC with steps smaller than window, each region in cpn will overlaps, for example:

1       7000    11999   4345
1       8000    12999   5076
1       9000    13999   5705
1       10000   14999   6582
1       11000   15999   3599
1       12000   16999   4017
1       13000   17999   4366
1       14000   18999   4473

so sum them all will be wrong.

Second you make complement segments with 0 copy number and NA marker_num. It's this necessary?

kunstner commented 2 years ago

Hi, I just use control-freec in combination with gistic for WXS data with window size set to 0. For WGS data I used a window size of 50k without any problems. Therefore, I do not know where the problem occurs in your case. To resolve this issue you should ask the developers of freec.

Regarding your second question, I think gistic needs a complete segment file (but I do not remember exactly). It doesn't hurt to include these 0 coverage regions anyway.

Best, Axel