Questions About the GISTIC2 Module output amp plot file

[Jihong Tang]

Hi,

I have some questions about the output file of the GISTIC2 Module. I used the GISTIC2 module offline and will get the amp_qplot.pdf and del_qplot.pdf files among the outputs. When I check the results for different cnv analysis jobs, I found that the display of the chromosome regions in different amp_qplot.pdf is different. As attached, the length of the two chr2 black blocks is different in two different analysis jobs. Therefore, I am wondering how the display style of the region of the chromosomes is determined. Are there any parameters that can control the display style? In other words, if I would like to make the display of the chromosome regions the same among different jobs, how can I achieve that? 

Thank you so much in advance for any suggestions and help!!!

Bests,
Jihong 

[Ted Liefeld]

For a question like this its best to consult the GISTIC forum (https://groups.google.com/a/broadinstitute.org/g/gistic-forum) where the authors and developers of GISTIC can respond.

Hope this helps,

Ted

[Jihong Tang]

Hi

Thank you for the instructions.

Best

Jihong 

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