Description

calculates scores per genome regions for other deeptools plotting utilities

Input

name:type
description
pattern

meta{:bash}

:map

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

bigwig{:bash}

:file

bigwig file containing genomic scores

*.{bw,bigwig}

bed{:bash}

:file

bed file containing genomic regions

*.{bed}

Output

name:type
description
pattern

matrix{:bash}

meta{:bash}

:map

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

*.mat.gz{:bash}

:file

gzipped matrix file needed by the plotHeatmap and plotProfile deeptools utilities

*.{computeMatrix.mat.gz}

table{:bash}

meta{:bash}

:map

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

*.mat.tab{:bash}

:file

tabular file containing the scores of the generated matrix

*.{computeMatrix.vals.mat.tab}

versions_deeptools{:bash}

${task.process}{:bash}

:string

The name of the process

deeptools{:bash}

:string

The name of the tool

computeMatrix --version | sed "s/computeMatrix //g"{: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

deeptools{:bash}

:string

The name of the tool

computeMatrix --version | sed "s/computeMatrix //g"{:bash}

:eval

The expression to obtain the version of the tool

Tools

deeptools
GPL v3

A set of user-friendly tools for normalization and visualization of deep-sequencing data

deeptools.readthedocs.io/en/develop https://github.com/deeptools/deepTools 10.1093/nar/gku365
included in
atacseqchipseqcutandrunsammyseq
maintainers
Github user jeremy1805
Github user edmundmiller
Github user drpatelh
Github user joseespinosa
get in touch
Ask a question on Slack Open an issue on GitHub