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:

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

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


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.