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