Question: Focal copy number alterations in IGV
gravatar for neuro3030
2.2 years ago by
neuro303010 wrote:

I am visualizing a segmented copy number file (.seg) from the TCGA in IGV.

From the example screenshot below, the gene RAC2 shows loss in a few samples (blue). Assuming all of the samples that are blue for RAC2 are significant using GISTIC, how do you interpret the sample with a portion of the gene in blue (sample is about midway down)?

For instance, assuming the raw score for the blue portion is -0.6552, and the white portion (corresponding to the other half of the gene) is -0.0054, how can you determine which portion of the gene is significantly deleted? Are both the blue and the white? Just the blue portion?

thanks and any help would be great

enter image description here

igv copy number tcga cna • 848 views
ADD COMMENTlink written 2.2 years ago by neuro303010

Did you try looking at the raw SCNA data from TCGA?

ADD REPLYlink written 2.2 years ago by RamRS30k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1022 users visited in the last hour