What input files does the software metilene accept/require to identify the DMR between groups for WGBS data?

Question

[331885030]

Hi everyone, I'm analyzing the WGBS data and found the software metilene could identify the DMR between groups. But I don't know what input files does the software metilene accept/require, if there are somebody could send me an example. Thank you very much.

Answer 1

[Devon Ryan]

Yeah the documentation isn't so great there. The basic format is what is shown in section 4 of the manual.

[331885030]

So firstly, I need to get the absolute methylation ratio for genome postion for all samples using another softwre, right?

[Devon Ryan]

Correct. You can get that with PileOMeth or whatever methylation extractor happens to come with the aligner you used.

[331885030]

Thank you very much. BTW, do you know the difference between the input files of DMR de-novo annotation and that of DMR annotation in known features?

[Devon Ryan]

I don't, sorry. If it's not clear from the documentation then you can email the authors.

[331885030]

Ok, I will. Thank you very much