Description

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

Input

name:type
description
pattern

peaks{:bash}

:list

BED, narrowPeak or broadPeak files of replicates

*

peak_type{:bash}

:string

Type of peak file

{narrowPeak,broadPeak,bed}

prefix{:bash}

:string

Prefix for output files

Output

name:type
description
pattern

idr{:bash}

*idrValues.txt{:bash}

:file

Text file containing IDR values

*.{txt}

log{:bash}

*log.txt{:bash}

:file

Log file

*.{txt}

png{:bash}

*.png{:bash}

:file

Plot generated by idr

*{.png}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
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