Description

Visualises sample correlations using a compressed matrix generated by mutlibamsummary or multibigwigsummary as input.

Input

name:type
description
pattern

meta{:bash}

:map

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

matrix{:bash}

:file

compressed matrix file produced by mutlibamsummary or multibigwigsummary

*.{npz}

method{:bash}

:string

Correlation coefficient to use for heatmap or scatterplot generation

{spearman,pearson}

plot_type{:bash}

:string

Type of output plot to display sample correlation

{heatmap,scatterplot}

Output

name:type
description
pattern

pdf{:bash}

meta{:bash}

:map

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

*.pdf{:bash}

:file

Output figure containing resulting plot

*.{plotCorrelation.pdf}

matrix{:bash}

meta{:bash}

:map

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

*.tab{:bash}

:file

Tab-separated file containing a matrix of pairwise correlations

*.{plotCorrelation.mat.tab}

versions_deeptools{:bash}

${task.process}{:bash}

:string

The name of the process

deeptools{:bash}

:string

The name of the tool

plotCorrelation --version | sed "s/plotCorrelation //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

plotCorrelation --version | sed "s/plotCorrelation //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
cutandrunsammyseq
maintainers
Github user tamara-hodgetts
Github user chris-cheshire
Github user joseespinosa
get in touch
Ask a question on Slack Open an issue on GitHub