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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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The color meaning of each line that appears when use the view option #268

Open BIjoy92 opened 2 years ago

BIjoy92 commented 2 years ago

Hello,

I would like to know the color meaning of each line that appears when I use the view option in cnvnator. image I found that black means coverage and green means segment, but I couldn't find what red means. Is that segment means CNVsize? then why appear on the line like in these figures? and what does red mean?

Here is the code I did to get this image: image

Thank you.

abyzov commented 2 years ago

Hi, red color represent segmentation before calling CNVs. RD signal for segments which don’t pass significance is averaged with the background. So, the final green segmentation is slightly different from red segmentation.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978