SimpleNexusCaller

SimpleNexusCaller calls ChIP-nexus peaks based on the commonly provided bedGraph input format. This is performed in 3 simple steps: 1) identification of 'signal' regions on the + and - strands, 2) identification of TF boundaries on the + and - strand indicated by the summit of a signal range, and 3) by matching the TF boundaries on the + strand to the closest TF boundary downstream on the - strand. See designNotes.txt to better understand the implimentation.

Install

Python3.x with the following packages:
Numpy
Pandas

To install from source:

git clone https://github.com/BradBalderson/SimpleNexusCaller.git
cd SimpleNexusCaller
python3 setup.py install

Usage

In the command line, type in 'simplenexuscaller -h ' for detailed usage.

$ simplexnexuscaller -h

usage: simplenexuscaller [-h] -i INPUT INPUT [-c CUTOFF] [-f FALSEINROWUPPER]
                     [-n NINROWCUTOFF] [-d DISTLIMIT] [-m MAXWIDTH]
                     [-o OUTPUT]

Takes ChIP-nexus data in bedGraph format for + and - strand and performs fast
and simple peak calling.

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT INPUT, --input INPUT INPUT
                        ChIP-nexus bedGraph files, where each column is [chr,
                        start, end, count], with no column headers. These
                        files must be in the order of counts on the + or -
                        strand. Inputs are separated by a single space. Each
                        BedGraph contains positions per base where counts
                        represent the number of 5' reads mapping to that
                        position. Where no reads mapped, position refers to
                        interval where no reads mapped.
  -c CUTOFF, --cutoff CUTOFF
                        Cutoff number of counts above which the
                        positionconsidered as having signal.
  -f FALSEINROWUPPER, --falseInRowUpper FALSEINROWUPPER
                        No. of no signal positions (count>cutoff) in row
                        before terminate extension of signal region.
  -n NINROWCUTOFF, --nInRowCutoff NINROWCUTOFF
                        The minimum length of a TF edge signal for thesignal
                        to be called as a true signal.
  -d DISTLIMIT, --distLimit DISTLIMIT
                        Minimum distance between signal range on the
                        samestrand for them to be considered the same or
                        differentTF binding signal edges.
  -m MAXWIDTH, --maxWidth MAXWIDTH
                        Maximum width a peak is allowed to be.
  -o OUTPUT, --output OUTPUT
                        Output filename prefix. Automatically adds .bed

Example

$ simplenexuscaller -i posCounts.bedGraph negCounts.bedGraph -o output_prefix

Output

Output will be in standard bed file format:

output_prefix.bed: The called peaks.

output_prefix.bed file has 3 columns. See the toy example below.

chr	start	end
chr1	9118	10409

Citation

Contact

Authors: Brad Balderson, Mikael Boden

Contact: brad.balderson@uqconnect.edu.au

BradBalderson / SimpleNexusCaller