Description

Summarize and/or filter reads based on bisulfite conversion rate

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 contained mapped reads

meta2{:bash}

:map

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

bai{:bash}

:file

BAM file index

meta3{:bash}

:map

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

fasta{:bash}

:file

Input genome fasta file

meta4{:bash}

:map

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

index{:bash}

:directory

Directory containing biscuit genome index

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

*.bam{:bash}

:file

Output BAM file containing filtered read alignments

*.{bam}

versions_biscuit{:bash}

${task.process}{:bash}

:string

The name of the process

biscuit{:bash}

:string

The name of the tool

biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'{: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

biscuit{:bash}

:string

The name of the tool

biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'{:bash}

:eval

The expression to obtain the version of the tool

Tools

biscuit
MIT

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

huishenlab.github.io/biscuit huishenlab.github.io/biscuit/docs/subcommand_help.html#biscuit-bsconv https://github.com/huishenlab/biscuit
maintainers
Github user njspix
Github user sateeshperi
get in touch
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