Description

“This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.”

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

Output

name:type
description
pattern

spp{:bash}

meta{:bash}

:map

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

*.out{:bash}

:file

A ChIP-Seq Processing Pipeline file containing peakshift/phantomPeak results

*.{out}

pdf{:bash}

meta{:bash}

:map

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

*.pdf{:bash}

:file

A pdf containing save cross-correlation plots

*.{pdf}

rdata{:bash}

meta{:bash}

:map

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

*.Rdata{:bash}

:file

Rdata file containing the R session

*.{Rdata}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

phantompeakqualtools
BSD-3-clause

"This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays."

github.com/kundajelab/phantompeakqualtools 10.1101/gr.136184.111
included in
chipseq
maintainers
Github user drpatelh
Github user edmundmiller
Github user JoseEspinosa
get in touch
Ask a question on Slack Open an issue on GitHub