nanoporetech
Using segmenting on differential methylation
Hello @ArtRand ,
I would like to compare the methylations of 2 conditions by regions and not by a specific position.
In the modkit dmr pair what should be the input for the --segments parameter? In the tutorial, you indicated dmr_segments=single_base_segements.bed, what is the format of this bed file? What does it mean single base segments? Can I search through all the genome and not only on specific regions?
Thanks for your help & patience for my basic questions, Raya
Hello @Raya-Faigenbaum-Romm,
The schema for the output segments table can be found in the documentation.
The argument is a file to write the data to, simply adding the file is all you need to do in order to tell Modkit to perform segmentation. It will perform segmentation (i.e. differential methylation region discovery) on all of the positions in the bedMethyl input files. No worries about the questions, happy to help.
Hello @ArtRand , Thanks for the explanation & help as always. Raya
@ArtRand it would be useful to update/fix the docs. In the page you pointed it's --segments, while the actual switch is --segment.
