Description

Computes read coverage for genomic regions (bins) across the entire genome.

Input

name:type
description
pattern

meta{:bash}

:map

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

bams{:bash}

:file

One or more BAM files

*.{bam}

bais{:bash}

:file

Corresponding BAM file indexes

*.bam.bai

labels{:bash}

:string

User specified labels instead of default labels (file names).

meta2{:bash}

:map

Groovy Map containing blacklist metadata e.g. [ id:‘blacklist’ ]

blacklist{:bash}

:file

BED/GTF file containing regions to exclude from analysis

*.{bed,gtf}

Output

name:type
description
pattern

matrix{:bash}

meta{:bash}

:map

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

*.npz{:bash}

:file

compressed numpy array of read coverage data used by plotCorrelation and plotPCA deeptool utilities

all_bam.bamSummary.npz

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

deeptools
GPL v3

A set of user-friendly tools for normalization and visualization of deep-sequencing data

deeptools.readthedocs.io/en/develop https://github.com/deeptools/deepTools 10.1093/nar/gku365
included in
cutandrun
maintainers
Github user tamara-hodgetts
Github user chris-cheshire
Github user joseespinosa
get in touch
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