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:false ]
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:false ]
*.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).
