How to draw venn diagram for two CNV lists?

Question

[lyz10302012]

I want to draw the venn diagram for two CNV lists. I use a 1-bp reciprocal overlap criterion to declare two CNVs are same.

My question is if one element in list 1 overlaps with multi elements in list 2, how can I interpret intersect?

i.e.

Size of list1: 100

Size of list2: 200

10 CNVs in list1 overlaps with 20 cnvs in list2

Here my question is how to determine the intersect, is it 10 ,20 or both? How can I draw the venn diagram?

[lyz10302012]

Here my question is how to determine the intersect, is it 10 or 20?

[sysbiocoder]

10 CNVs in list1 overlaps with 20 cnvs in list2 It means there are duplicates in list. While drawing Venn we consider only unique values. Hope I answered your question

Answer 1

[Jie Ping]

The website may help you.

http://bioinfogp.cnb.csic.es/tools/venny/index.html

[InterestedScientist]

Venny was down today... In any event, I would highly recommend I would highly recommend VENDIS.

It just came out and it's really quite good!

Answer 2

[Rodons]

You can also use biovenn, which will also recognize your entries and will link them.

Answer 3

[David Westergaard]

I am not a CNV expert (or genomics, for that matter), but I think it boils down to the question you are asking. Are you counting the number of overlapping CNVs when comparing sample 1 to sample 2, or sample 2 to sample 1? I think both would be fine, as long as you make sure to write which comparison you are making.

Answer 4

[NB]

You can easily do it in R but if you want to opt for a software, I find this tool very useful http://omics.pnl.gov/software/venn-diagram-plotter

Answer 5

[Malachi Griffith]

Here is a good StackOverflow post on creating Venn diagrams in R.

Answer 6

[shalin]

Its probably best to use use a Venn Diagram Maker like Creately. Its an online diagramming & collaboration software to draw Venn diagrams. There are all the objects and shapes necessary to create Venn and Euler diagrams with 100s of templates and examples to be used freely.

Answer 7

[lieven.sterck]

And here is another alternative (draws up to 6 intersections): Draw Venn