Description

Extracts per-base methylation metrics from alignments

Input

Name (Type)
Description
Pattern

meta (map)

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

]

fasta (file)

Input genome fasta file

*.{fasta,fa}

fai (file)

FASTA index file

*.fai

bam (file)

BAM/CRAM file

*.{bam,cram}

bai (file)

BAM/CRAM index file

*.{bai,crai}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bedgraph (file)

bedGraph file, containing per-base methylation metrics

*.bedGraph

methylkit (file)

methylKit file, containing per-base methylation metrics

*.methylKit

versions (file)

File containing software versions

versions.yml
included in
methylseq
author
Github user phue
get in touch
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Tools

methyldackel
MIT

Methylation caller from MethylDackel, a (mostly) universal methylation extractor for methyl-seq experiments.

github.com/dpryan79/MethylDackel github.com/dpryan79/MethylDackel/blob/master/README.md