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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

spp (file)

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

*.{out}

pdf (file)

A pdf containing save cross-correlation plots

*.{pdf}

rdata (file)

Rdata file containing the R session

*.{Rdata}
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

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