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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
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CNV summary missing? #625

Closed olechnwin closed 5 years ago

olechnwin commented 5 years ago

Hi,

I am trying to view SEG file in IGV. I modified the cbs file generated by varScan to match the example.seg in the IGV manual SEG file format. I cannot figure out why my modified file test_1 (in IGV) does not have CNV summary while the example.seg file does. seg_visual

Can someone tell me why ?

I'm attaching my file: test.seg and the example from IGV: example.seg in the zip file: seg_files.zip Thank you in advance for your help!

jrobinso commented 5 years ago

The test.seg file has a single sample, so there is nothing to summarize.

On Tue, Feb 12, 2019 at 9:38 AM olechnwin notifications@github.com wrote:

Hi,

I am trying to view SEG file in IGV. I modified the cbs file generated by varScan to match the example.seg in the IGV manual SEG file format https://software.broadinstitute.org/software/igv/SEG. I cannot figure out why my modified file test_1 (in IGV) does not have CNV summary while the example.seg file does. [image: seg_visual] https://user-images.githubusercontent.com/20069067/52655707-cf6bea80-2ec2-11e9-9266-4de9693cab4a.png

Can someone tell me why ?

I'm attaching my file: test.seg and the example from IGV: example.seg in the zip file: seg_files.zip https://github.com/igvteam/igv/files/2856893/seg_files.zip Thank you in advance for your help!

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olechnwin commented 5 years ago

ahhh.....duh! I kept thinking that was the genome location summary. It couldn't be. Duh! Thanks, Jim! Sorry for my idiocy but thank you so much for your quick response.