March 20, 2013

Scope of Reduced Representation Bisulfite Sequencing Data

RRBS method explores the methylation status across the genome but at specific locations defined by the MspI recognition sites. These sites are mostly located within CpG Islands. So, how to visulaize the scope of the RRBS data - regions from where we can expect the methylation status in the human genome.

I show the localization of the CpG Island on the human genome in the following graphic. These are the most possible locations for the RRBS data sampling

This is a Karyogram view of the CpG Island on human chromosomes. Chromosomes were plotted relative to their size. Each CpG island is denoted by a single dot at the relative position on the chromosome. CpG Island close to each other are perceived as a connecting line to the human eye (hundred of dot placed closely). This picture also gives us an Idea that certain parts of the chromosomes either lack CpG islands (chr1, chr13, chr14, chr15). This could be due to incomplete mapping of human genome on these chromosomes.

I made this graphic using ggbio and ggplot2.
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