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:map

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

]

bam:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

Output

name:type
description
pattern

spp

meta:map

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

]

*.out:file

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

*.{out}

pdf

meta:map

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

]

*.pdf:file

A pdf containing save cross-correlation plots

*.{pdf}

rdata

meta:map

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

]

*.Rdata:file

Rdata file containing the R session

*.{Rdata}

versions

versions.yml: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."