how to overlap cnvs to cnv region automatically？and how to draw a chromosome map of cnvrs？ thanks

Question

[yanjuncong]

Hi there

I have got several thousands cnvs and want to merge them into cnvrs, besides when I got the cnvs, I want to map them in a chromosome. who can help me

Thanks a lot

john

[Pierre Lindenbaum]

Did you search biostars.org to answer your question? What did you find?

[yanjuncong]

Yes, just one blog called "map cnv". but the answer is not ok. I have no idea about R and I also have no idea about galaxy. I need to submit my paper this week which made me crazy. I used a software called cnvruler to overlap my data. however, there is X Y chromosome showed in the result. I have deleted all the cnvs on X & Y which made me so confused. so I want to look for another software to double check it. if you can help me I will very appreciate.

Answer 1

[lomolith]

Hi, I'm the author of CNVRuler (which I'll change the name soon, though). Sorry, I couldn't find this question till today.

I assume you used old version of it and your data was non-human. You can download the latest version of this from here

Let me know if you still have a problem.

[yanjuncong]

Hi lomolith

Thanks for your help, I will try to use it.

John

[yanjuncong]

Hi lomolith

I have tried the software you gave to me. it can calculate the data from CNVpartition and Penncnv directly. It's great, however, it looks cannot read the data I made manually. I tried to build a file like the manual of your software, setting up 5 columns . But I do not know why it cannot be read. Could you give your email address, I can send it to you directly.

Thanks a lot

John

Answer 2

[jglessnd]

Try ParseCNV. Given the output, you can use UCSC Genome Graphs to draw them on chromosomes.