RoAM: Reconstruction of Archaic Methylation
written by: David Gokhman, Eitan Lavi, Liran Carmel
RoAM allows reconstruction of high-resolution, genome-wide, methylation maps from high-coverage
ancient DNA sequencing data. The software computes a C->T ratio for all CpGs in the genome and
will find the optimal window for sliding the data, based on measurements of modern methylation
map. Lastly, the C->T ratio will be translated to inferred archaic methylation. The software is
now design to reconstruct methylation along archaic human, but will be updated in the future to
work on any genome.
The software is written in Matlab, and you run it by just typing
At the current version, RoAM does not require input parameters.
RoAM is freely available (tested under Windows XP), and can be downloaded by clicking the
The output is in the form of Matlab data files of the syntax out(chr number).mat. For example: chr1.mat,
chr2.mat, etc. Each file contains the position of the cytosine (in CpG context) along the respective
chromosome, and its reconstructed methylation level.