RoAM: Reconstruction of Archaic Methylation

written by: David Gokhman, Eitan Lavi, Liran Carmel

last modified:

General Description
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
RoAM. 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 download button download.

Output Files
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.