GISTIC output files

[rocio...@gmail.com]

Dear all,

I am a Bioinformatics student working on a project in which I need to use level 4 CNV data.

For that purpose I downloaded the GISTIC2 output files for a particular cancer in the appropriate website. However, I am quite confused about which file should I be using.

At the beginning I thought the al_thresholded_by_genes.txt was the one, however, is that one filtering out those focal and broad aberrations not found to be significant? If it does not, which files should I use. I've look for answers in the forum and read the documentation but I don't think it is a 100 % clear yet.

Thanks in advance,

Rocio.

[Michael Noble]

Hi Rocio,

Thank you for using our work.  For your cohorts of interest I would check the corresponding GISTIC analysis report on FireBrowse, in conjunction with reading the GISTIC paper that is referenced at the bottom of those reports.  Lastly, the Copy Number sections of the FireBrowse API also describe the output files to some degree.  After looking at all of these, If you're still unclear about what files you want to use then just let us know.

Best,

Mike

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Michael S. Noble

Associate Director for Data Science

Cancer Genome Computational Analysis

The Broad Institute of MIT & Harvard