Description

Extracts methylation information for individual cytosines from alignments.

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM file containing read alignments

*.{bam}

meta2{:bash}

:map

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

index{:bash}

:directory

Bismark genome index directory

BismarkIndex

Output

name:type
description
pattern

bedgraph{:bash}

meta{:bash}

:map

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

*.bedGraph.gz{:bash}

:file

Bismark output file containing coverage and methylation metrics

*.{bedGraph.gz}

methylation_calls{:bash}

meta{:bash}

:map

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

*.txt.gz{:bash}

:file

Bismark output file containing strand-specific methylation calls

*.{txt.gz}

coverage{:bash}

meta{:bash}

:map

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

*.cov.gz{:bash}

:file

Bismark output file containing coverage metrics

*.{cov.gz}

report{:bash}

meta{:bash}

:map

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

*_splitting_report.txt{:bash}

:file

Bismark splitting reports

*_{splitting_report.txt}

mbias{:bash}

meta{:bash}

:map

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

*.M-bias.txt{:bash}

:file

Text file containing methylation bias information

*.{M-bias.txt}

versions_bismark{:bash}

${task.process}{:bash}

:string

The name of the process

bismark{:bash}

:string

The name of the tool

bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

bismark{:bash}

:string

The name of the tool

bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'{:bash}

:eval

The expression to obtain the version of the tool

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
included in
methylseq
maintainers
Github user phue
Github user sateeshperi
get in touch
Ask a question on Slack Open an issue on GitHub