Introduction

modiff looks for differentially methylated loci.

It's work in progress and I'm still testing it, do not use.

By default it does a two group tests by using Bayes factors with a binomial model for the counts. Other models can be specified.

Usage is as folllows:

modiff FILE

where FILE can either be:

• A TAB-separated file containing modified bases counts. The columns are contig and genomic coordinate followed by depth and number of modified bases per each sample. For example with 2 samples an input line looks like the following:

  chr1\t10471\t20\t7\t23\t19

  In this case modiff can read directly from the stdin if the file name is -.

or

• a bgzip compressed, tabix indexed TAB-separated file, organized as above. the tabix format is automatically recognized by modiff.

Options

Models

• logreg corresponds to running a binomial logistic regression with an intercept term and a group term, and testing the significance of the group term

output format

modiff produces an output file compliant with the BEDn specifications https://samtools.github.io/hts-specs/BEDv1.pdf (0-based, half open coordinate system).

The output format changes depending on the model used, but the first few columns are always the same.

column	quantity	comment
1	contig/chromosome	reference sequence
2	start position	(inclusive, 0-based)
3	end position	(exclusive, 0-based)
4	mean methylation by group	comma separated
5	depth by group	comma separated

in the other model the other columns are to be documented but the last column always contain an indicator of strenght of effect or significance (pvalue or Bayes factor).

Contact

github issues and/or pull requests. email to emanuele dot raineri at cnag dot eu