Introduction

How to install

see Installation or Build from source.

Quick start guide

Make sure DBPnet executable is in your system path. Type DBPnet --help to see available command line options.

Preparing input data for DBPnet

ChIP-seq samples

DBPnet analyzes aligned tag files in BED format to create the network. To start, write down all samples in a new yaml file. Here is a example:

example.yaml
------------
- target: CTCF
  files:
      - path: path-to-data/CTCF.bed.gz
      - format: BedGZip

- target: RAD21
  files:
      - path: path-to-data/RAD21.bed
      - format: Bed

Note

All fields are case sensitive. If the format is not specified, DBPnet will try to guess the correct format based on the file names.

Chromosome size file

This is a file describing the sizes of each chromosome. Example:

chr1 [Tab] 249250621
chr2 [Tab] 243199373

You need to provide this file to DBPnet through the command line option --chrom_size <FILENAME>. For your convenience, DBPnet includes some common genome size (hg19 and mm10). You can use them by --chrom_size hg19.

Chromosome long range interactions (Optional)

This is an optional input for DBPnet. It is a 6-field Tab-separated file, and each line consists of two genomic loci that form a loop. For example:

chr1 [Tab] 10000 [Tab] 11000 [Tab] chr1 [Tab] 20000 [Tab] 21000

Running DBPnet

  • With a loop file:
DBPnet samples.yaml --loop loops.tsv --output DBPnet_output --chrom_size hg19

The results, including 2D and 3D cooperation, will be saved to directory DBPnet_output.

  • Without a loop file:
DBPnet samples.yaml --output DBPnet_output --chrom_size hg19

The results, only 2D cooperation, will be saved to directory DBPnet_output.

An example data set is available in Demo.