What are the best tools for visualizing DNA methylation result?

Question

[ahmad mousavi]

Hi

I have analyzed RRBS data, in this phase I look for good tool for visualizing genomic position of DMRs.

What tool you suggest for visualizing methylation result based on bed file or coverage file made by Bismark?

I wanted to create figure contains methylation position along with TSS, Promoter and gene body ? I have seen homer but I couldn't find out which parameter should be assign for showing genomic sections (TSS,TTS, promoter , ...)

Thanks

Answer 1

[Antonio R. Franco]

Take a look to these utilities. They have graphical output of your interest

1. methgo. Make it easy to study methylation in different parts of the genome if you provide a gtf file
2. CGmaptools. It contains 40 utilities, letting you to evaluate from mbias to DMR, and bin graphics

[ahmad mousavi]

Dear Antonio, Thank you so much. I have used CGmaptools and methgo, but during running methgo met function I have got this error, do you have any idea about that?

Thanks.

Traceback (most recent call last):
  File "/home/gen/apps/methgo/methgo", line 13, in <module>
    module.main()
  File "/home/gen/apps/methgo/scripts/met/met.py", line 410, in main
    cgmap = const_cgmap(ctxstr, args.cgmap, args.depth)
  File "/home/gen/apps/methgo/scripts/met/met.py", line 97, in const_cgmap
    pos = int(line[2]) - 1 # Transfer to 0-based
ValueError: invalid literal for int() with base 10: 'mv'

[nathan.alary]

Hi Ahmad,

I see your post is 9 weeks old but I will try.

I get the exact same error :

" File "/home/gen/apps/methgo/scripts/met/met.py", line 97, in const_cgmap pos = int(line[2]) - 1 # Transfer to 0-based ValueError: invalid literal for int() with base 10: 'mv' "

I assume you injected your CGmap file into methgo met function (obtained with CGmaptools) and got this error. I have exactly the same problem. Did you find a solution ?

Thank you :)

[ahmad mousavi]

Dear Nathan,

I'm sorry, I couldn't solve it. :(

[karyowgene]

try to decompress the CGmap.gz

Answer 2

[GenoMax]

deepTools should be on your list. Plenty of tutorial/help materials available.

Answer 3

[xieshaojun0621]

You can also try ViewBS: https://github.com/xie186/ViewBS