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bismark2bedGraph

By Krueger F., Andrews S.R., Last update 1494699000
All tools Run in Terminal

bismark2bedGraph description

bismark2bedGraph uses positional methylation data generated by the Bismark methylation extractor to generate a bedGraph file which is sorted by chromosomal position. bedGraph files use 0-based genomic coordinates and should be UCSC compatible (if UCSC genomes were used for the alignment step). It is also possible to choose the option counts to output the count of methylated and unmethylated cytosines for any covered position


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