Hi everyone!
I have DamID data for two conditions in the form of the log2 methylation ratio of Dam LaminB1 to Dam Only, from this publication (https://genome.cshlp.org/content/27/10/1634.full).
The distribution of windows for the data are in and around 1mb, and there are about 28000 data points.
head(DamID_OIS)
chr start end ratio
chr1 764621 864620 -0.7687818
chr1 864621 964620 -0.9207849
chr1 964621 1064620 -0.9493541
chr1 1064621 1164620 -0.8203121
chr1 1164621 1264620 -1.6871681
chr1 1264621 1364620 -1.6889285
From what I understand, positive values would mean that the region is attached to the lamina, based on the methylation ratio. But the range of the positive values is quite large (~15000). From this list, how can I call boundaries of Lamina Associated Domains? Should I just take higher values based on some quantile percentage, or asses the AT content of the regions and concatenate high AT regions? Or is there a tool/caller that does the job?
Thanks in advance!
Rishi
