coverage2cytosine generates a cytosine methylation report for a genome of interest and a sorted methylation input file produced by the script bismark2bedGraph. By default, the output uses 1-based chromosome coordinates and reports CpG positions only (for both strands individually and not merged in any way). Coordinates may be changed to 0-based using the option zero_based.
Parent program: bismark
Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. Its main features are: (1) bisulfite mapping and methylation calling in one single step; (2) Supports single-end and paired-end read alignment; (3) Supports ungapped and gapped alignments (4) Alignment seed length, number of mismatches etc. are adjustable (5) Output discriminates between cytosine methylation in CpG, CHG and CHH context