GISTIC2, some missing samples during the process

Question

[jgarces]

Hi everyone, I'm running GISTIC2 (the version 2.0.23, through commands) with some samples present in my SEG file that dissapear totally in the final object (all_lesions.conf_90.txt).

During the process, it appears the following warning: "Shortened 234569 segments in 'filePath' that overlap by one marker" but I don't know if this is causing this problem or it comes from another point... And a possible way to solve it in case you identified the error!

Any idea, please? Thanks in advance.

Answer 1

[Kevin Blighe]

Hola, cómo estás? - todo bien? Can you show the commands that you are using for GISTIC? You looked at the manual pages to see what are the default parameters? Me puede mostrar una parte de sus datos que está usando con GISTIC?

[jgarces]

Hi Kevin, you're right with the defaults parameters... I missed the -maxseg one and some samples had more segments that the default value. Sorry for this silly error. Thanks a lot!

[Kevin Blighe]

De nada - no te preocupes