Description

Create a tag directory with the HOMER suite

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM/BED/SAM file

*.{bam,bed,sam}

fasta (file)

Fasta file of reference genome

*.fasta

Output

Name (Type)
Description
Pattern

meta (map)

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

]

tagdir (directory)

The “Tag Directory”

*_tagdir

taginfo (directory)

The tagInfo.txt included to ensure there’s proper output

*_tagdir/tagInfo.txt

versions (file)

File containing software versions

versions.yml
included in
nascent
author
Github user EMiller88
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Tools

homer
GPL-3.0-or-later

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.

http://homer.ucsd.edu/homer 10.1016/j.molcel.2010.05.004.

samtools
MIT

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352

DESeq2
LGPL-3.0-or-later

Differential gene expression analysis based on the negative binomial distribution

bioconductor.org/packages/DESeq2 https://github.com/mikelove/DESeq2 10.18129/B9.bioc.DESeq2

edgeR
GPL >=2

Empirical Analysis of Digital Gene Expression Data in R

bioinf.wehi.edu.au/edgeR bioconductor.org/packages/edgeR https://git.bioconductor.org/packages/edgeR 10.18129/B9.bioc.edgeR