Set and display CNV summary tracks

[fabrice sircoulomb]

Hi,

I am using IGV 2.1 and want to dispaly the "CNV summary" track for my CBS data to see the frequency plot.

By default when I am opening IGV the CNV summary track is not present.

I looked at the IGV website and in the forum but did not find any explanations on how to set this specific track.

Could you briefly guide me on that?

Best,

Fab

[fabrice sircoulomb]

I figure out the problem.

The CNV summary track is only automatically activated when you load a .seg file containing a all your samples.

It is not working if you load individually the .seg files for each samples.

Fab

[Lara Nonell]

Dear Fabrice and the rest,

I would like to include also de CNV summary track but it is not automatically created. I tried loading the example.seg file and no summary appeared. I checked IGV's options and did not find it either

Do you know how to create it automatically? I would like to use it to summarize my CNV results

Thanks!

LAra

El dimarts, 22 gener de 2013 18:56:42 UTC+1, fabrice sircoulomb va escriure:

[Jim Robinson]

Hi,

The summary track only appears if you have 5 or more samples in the file, the example has only 2.   Here's another example, you should see it with this one:  http://igvdata.broadinstitute.org/data/hg18/tcga/gbm/gbmsubtypes/Broad.080528.subtypes.seg.gz

Jim

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[Lara Nonell]

Dear Jim,

I have installed version 2.3.75 and now the summary track appears for only 4 samples so I guess this minimum has been changed, which is now the minimum?, would be great if it was just two.

Cheers!

Lara

El dijous, 5 maig de 2016 17:33:51 UTC+2, Jim Robinson va escriure:

[Jim Robinson]

The minimum now is 2,  so I'm not sure what the cause of this could be.    Is it possible to attach a small .seg file that is exhibiting the problem?

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