Brockman: Brockman Representation Of Chromatin by K-mers in Mark-Associated Nucleotides

Overview

What is Brockman?

Brockman is a suite of command line tools and R functions to convert genomics data into DNA k-mer words representing the regions associated with a chromatin mark, and then analyzing these k-mer sets to see how samples differ from each other. This approach is primarily intended for single cell genomics data, and was tested most extensively on single cell ATAC-seq data. The bash scripts in particular may require some alteration for other types of genomics data.

A preprint describing the approach is available here.

What are Brockman’s dependencies?

The command line tools rely on the following, and assume the shell is Bash:

• Ruby
• AMUSED: for counting k-mers
• BEDTools: For working with BED files
• Kent Tools - twoBitToFa: For extracting genomic sequence
• SAM Tools: For working with BAM/SAM files
• Trimmomatic: For trimming sequencing reads

The R analysis tools rely on the following packages:

• jackstraw
• ggplot2
• tsne

Installation

Command line tools

At present, only anaconda installation is supported. If you haven’t yet learned how to use anaconda, there’s no time like the present!

Linux/OSX:

conda create -c bioconda -n BrockmanEnv  brockman-pipeline

R library

If you don’t already have devtools, install it:

install.packages("devtools")

Load devtools and install from the GitHub page:

library(devtools)
install_github("Carldeboer/BrockmanR")

Usage

Command line tools

See Brockman_pipeline Example for example data processing pipelines.

R library

See Brockman Analysis Example for example analysis pipelines.

Citation

Please cite BROCKMAN if you find Brockman useful.

Carl G. de Boer, Aviv Regev. BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization. BMC Bioinformatics. (2018) 19:253;