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By Krueger F., Andrews S.R., Last update 1494699000
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bismark_methylation_extractor description

bismark_methylation_extractor script operates on Bismark result files and extracts the methylation call for every single C analysed. The position of every single C will be written out to a new output file, depending on its context (CpG, CHG or CHH), whereby methylated Cs will be labelled as forward reads (+), non-methylated Cs as reverse reads (-). The resulting files can be imported into a genome viewer such as SeqMonk (using the generic text import filter) and the analysis of methylation data can commence. Alternatively, the output of the methylation extractor can be transformed into a bedGraph file using the option --bedGraph

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