Description

Call peaks using SEACR on sequenced reads in bedgraph format

Input

name:type
description
pattern

meta:map

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

]

bedgraph:file

The target bedgraph file from which the peaks will be calculated.

ctrlbedgraph:file

Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.

threshold:integer

Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph

Output

name:type
description
pattern

bed

meta:map

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

]

*.bed:file

Bed file containing the calculated peaks.

*.bed

versions

versions.yml:file

File containing software versions

versions.yml

Tools

seacr
GPL-2.0-only

SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by "zeroes" (i.e. regions with no read coverage).