Description

Perform basic quality control on a BAM file generated with Biscuit

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 produced using Biscuit

meta2{:bash}

:map

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

fasta{:bash}

:file

Input genome fasta file

meta3{: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

reports{:bash}

meta{:bash}

:file

Summary files containing the following information:

  • CpG retention by position in read
  • CpH retention by position in read
  • Read duplication statistics
  • Insert size distribution
  • Distribution of mapping qualities
  • Proportion of reads mapping to each strand
  • Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT
*.txt

*.txt{:bash}

:file

Summary files containing the following information:

  • CpG retention by position in read
  • CpH retention by position in read
  • Read duplication statistics
  • Insert size distribution
  • Distribution of mapping qualities
  • Proportion of reads mapping to each strand
  • Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT
*.txt

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-qc https://github.com/huishenlab/biscuit
maintainers
Github user njspix
Github user sateeshperi
get in touch
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