Description

Measures reproducibility of ChIP-seq, ATAC-seq peaks using IDR (Irreproducible Discovery Rate)

Input

name:type
description
pattern

meta

:map

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

peaks

:list

BED, narrowPeak or broadPeak files of replicates

*

peak_type

:string

Type of peak file

{narrowPeak,broadPeak,bed}

Output

name:type
description
pattern

idr

meta

:map

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

*idrValues.txt

:file

Text file containing IDR values

*.{txt}

log

meta

:map

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

*log.txt

:file

Log file

*.{txt}

png

meta

:map

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

*.png

:file

Plot generated by idr

*{.png}

versions_idr

${task.process}

:string

The name of the process

idr

:string

The name of the tool

idr --version |& sed '1!d;s/^.*IDR //'

:eval

The expression to obtain the version of the tool

versions_python

${task.process}

:string

The name of the process

python

:string

The name of the tool

python --version |& sed 's/Python //'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

idr

:string

The name of the tool

idr --version |& sed '1!d;s/^.*IDR //'

:eval

The expression to obtain the version of the tool

${task.process}

:string

The name of the process

python

:string

The name of the tool

python --version |& sed 's/Python //'

:eval

The expression to obtain the version of the tool

Tools

idr
GPL v2

The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.

https://github.com/kundajelab/idr
maintainers
Github user drpatelh
Github user joseespinosa
get in touch
Ask a question on Slack Open an issue on GitHub