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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Visualize multiple chromsomes at once? #267

Open tania-k opened 2 years ago

tania-k commented 2 years ago

Hello CNVnator group, Thank you for a wonderful program. Your instructions have been straightforward and easy to follow with some trial and error. As I am visualizing the results I am curious if you can visualize more than one chromosome at a time?

I attempted this using the EOF option. cnvnator -root Ex15.all.root -view 1000 << EOF

chr1:1-75500 chr2:75701-213800 EOF But this gave a really wonky figure. I would like to visualize all of the genome/chromosomes if possible? Or at least 3 at a time, kind of in a sliding-window style.

Thank you for your time! Tania

abyzov commented 2 years ago

Hi, unfortunately CNVnator does not have functionality to visualize multiple regions. But you can used CNVpytor (the successor of CNVnator) which does have such a functionality.

https://github.com/abyzovlab/CNVpytor

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