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_scramble
${task.process}
:string
The name of the process
scramble
:string
The name of the tool
1.3
:string
The expression to obtain the version of the tool
versions_bedtools
${task.process}
:string
The name of the process
bedtools
:string
The name of the tool
bedtools --version | sed -e 's/bedtools v//g'
:eval
The expression to obtain the version of the tool
versions_rbase
${task.process}
:string
The name of the process
r-base
:string
The name of the tool
R --version | sed '1!d; s/.*version //; s/ .*//'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
scramble
:string
The name of the tool
1.3
:string
The expression to obtain the version of the tool
${task.process}
:string
The name of the process
bedtools
:string
The name of the tool
bedtools --version | sed -e 's/bedtools v//g'
:eval
The expression to obtain the version of the tool
${task.process}
:string
The name of the process
r-base
:string
The name of the tool
R --version | sed '1!d; s/.*version //; s/ .*//'
:eval
The expression to obtain the version of the tool
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).
