What are the best tools for visualizing DNA methylation result?

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

rrbs methylation rna-seq

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updated 3.8 years ago by karyowgene •

• written 8.1 years ago by ahmad mousavi

3 answers

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

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

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written 8.1 years ago by Antonio R. Franco

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'

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written 8.1 years ago by ahmad mousavi

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 :)

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written 7.9 years ago by nathan.alary •