visual comparison of CNV data

Question

[aharnishi02]

I am working on results of CNV studies obtained form an online database. I have the start and end co-ordinates of CNVs of several individuals. I want to visualize and compare all of them chromosome wise and identify the CNV regions common in all the individuals. How do I go about this? Is there an online software which would allow this? PS: I am not a trained bioinformatician.

Answer 1

[Denise CS]

You can also attach this data to the Ensembl Browser as explained in this tutorial page. You will have your data in a format like 'chr start end individual' (i.e. BED format) and you can compare it to our gene annotation, our variation data (variants annotated according to consequence terms), and regulation data from ENCODE, Blueprint and Roadmap projects (for annotation of enhancer promoter, CTCF, etc). We also include the CNVs from 1000 Genomes and structural variants from DECIPHER (see the region where PRR29 is anntoated). Once you attach your data, you also have the option to share that visualisation with your colleagues and collaborators. You just send them the URL we generate and they will see your data against our annotation.

[aharnishi02]

Extremely helpful suggestion, I tried it and it works perfectly well.

Answer 2

[QVINTVS_FABIVS_MAXIMVS]

UCSC Genome Browser is great for CNV visualization. Click on the "Custom Tracks" link under the "My Data" tab on the top of the page.

Make sure your CNVs are in BED format (or any other format UCSC can take). Either copy and paste or upload your file in the Custom Tracks page.

You can color the CNVs according to UCSC's formatting rules

[aharnishi02]

Thank you very very much. Your suggestion was extremely helpful!