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I have to compare the overlap or shared regions for 5 bed files and make a venn diagram of the overlapped regions.

I can use pybedtools but it's for 3 files max. Or I found http://bioinformatics.psb.ugent.be/webtools/Venn/

It's look like a good tool but I have any idea how I can code my data for found the overlap.

Or maybe someone have an R package?

Timur Shtatland
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Nono_sad
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    http://stackoverflow.com/help/how-to-ask – StefanS Mar 31 '16 at 14:31
  • Welcome to StackOverflow. Please read our [ask] page for hints on how to improve your question. Great question tend to provide quicker, better answers from the community – blurfus Apr 01 '16 at 00:11
  • There are many posts regarding Venn at biostars.org, for example this one: https://www.biostars.org/p/77362/ – zx8754 Apr 05 '16 at 07:27

2 Answers2

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I do not think you can call what you are asking for a Venn diagram. Suggest breaking the comparisons down to not more than three at a time and use area proportional ellipses to get a good enough approximation. (It looks like the link you have is a similar tool)

tomc
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The link you included can do what you ask, you simply need to ask it to add more files to fit your set of five.

I just used the "list" version, and it did a fine job with diagramming five distinct points, However, it needs it listed as one data point entry per line. I just used the alphabet as an example.

List one: (named it vowels)

a

e

i

o

u (remember one letter per line)

List two: cat

c

a

t

List three: cry

c

r

y

Now, click the add another list button....

List four: dog

d

o

g

List five: fish

f

i

s

h

Then calculate, and if you scroll to the bottom of the results, you get text specific mappings for each union, and the contents.

Names total elements cat vowels 1 a

cat cry 1 c

dog vowels 1 o

fish vowels 1 i

cat 1 t

dog 2 d g

vowels 2 e u

fish 3 s h f

cry 2 r y

Bee Kay
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  • Thanks you for your response, Yes it's work but with simply data. Me, I have some files like this : Chr Start End 1 143274104 143274337 Y 10001 10038 Y 12798 12817 And I have 5 files with somethink like 40.000 lines. And I have to check the overlap between the files and make it at the intersection of circle. So I don't know how I can do for this. Thanks you – Nono_sad Apr 01 '16 at 07:41