Description

Extracts methylation information for individual cytosines from alignments.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

BAM file containing read alignments

*.{bam}

index (directory)

Bismark genome index directory

BismarkIndex

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bedgraph (file)

Bismark output file containing coverage and methylation metrics

*.{bedGraph.gz}

methylation_calls (file)

Bismark output file containing strand-specific methylation calls

*.{txt.gz}

coverage (file)

Bismark output file containing coverage metrics

*.{cov.gz}

report (file)

Bismark splitting reports

*_{splitting_report.txt}

mbias (file)

Text file containing methylation bias information

*.{M-bias.txt}

versions (file)

File containing software versions

versions.yml
included in
methylseq
maintainer
Github user phue
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

bismark
GPL-3.0-or-later

Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.

github.com/FelixKrueger/Bismark github.com/FelixKrueger/Bismark[...]Docs 10.1093/bioinformatics/btr167