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

meta (map)

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

]

bed (file)

Bed file containing the calculated peaks.

*.bed

versions (file)

File containing software versions

versions.yml
included in
cutandrun
author
Github user chris-cheshire
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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).

github.com/FredHutch/SEACR