Hi, I have list of 8 TF's and they bind to various enhancers in the genome.

I have this data in excel and now I want to make a matrix where I want to see

TF A+B= X number of enhancers,

TF A+B+C= X +/- n number of enhancers,

Finally I want to cluster everything

can anyone help?

Thanks

Thanks,

I tried Cluster3, but I dont I believe I have to download UniConvertor to get the data. I tried downloading this but I couldn't because it require some additional software package sk1.

I am trying with intersectBed but looks like it runs on 'R' and I have to accept that this is the first time I am trying to use this 'code' language. In my PhD I spend 6 yrs on bench and now I need to do these analysis.

intersectbed will not run on R. it will work on unix command line. (See here)

Cluster 3.0 is easy to download as a GUI application on Windows/Mac. Why do you have to download Uniconvertor ? ( ps. I dont know what Uniconvertor is)

ps. this thread -How To Make Visual Graphs To Represent Common Transcription Factor Binding Sites In Different Enhancers? might help if you can get R working for you.

It would be easier if you would show us how your data looks like. Can you update your question?