A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing.

Features

DANPOS provides different tools to analyze chromatin feature in different manner:
• dpos analyzes changes in the location, fuzziness, and occupancy at each nucleosome or protein binding position. The functions is designed to analyze nucleosomes, but can be also very useful for analyzing other proteins whose binding pattern is similar to that of nucleosome, such as the protein MeCP2.
• dpeak analyzes change in width, height and total signal of each enriched peak. A peak may contains multiple positions. This function is designed to analyze transcription factor and is also useful for defining some histone modification peaks.
• dregion analyzes change in width, summit height, and total signal in each enriched region between samples. A region may contains multiple peaks, this function is designed to analyze chromatin features such as the histone modification H3K4me3.
• dtriple is a combination of the Dpos, Dpeak, and Dregion functions. When there is no knowledge about characteristics of the sequencing target, this function provide users a way to try all the three algorithms above.
• profile is a tool in DANPOS for analyzing the distribution of a chromatin feature flanking each given group of genomic sites or regions.
• stat is a tool in DANPOS to do statistical analysis for positions, peaks, or regions.
• wiq is a tool in DANPOS to do genome wide quantile normalization for data in wiggle format file.
• wig2wiq is a tool for converting .wig format file to .wiq format.

References:

• Kaifu Chen, etc. DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing.Genome Research. 2012. doi:10.1101/gr.142067.112 PubMed |  PMC |  Journal

• DANPOS Main Site:Main Site
• DANPOS Github:Github

• Module Name: DANPOS (see the modules page for more information)
• Current DANPOS command lines could be run as:

  	danpos.py -h
  

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load DANPOS
[user@cn3144 ~]$ danpos.py --help
danpos version 3.0.0
For help information for each function, try:
python danpos.py  -h

Functions:
	dpos:
		analyze each protein-binding position (~100
		to ~200bp wide) across the whole genome,
		e.g. nucleosome positions.
	dpeak:
		analyze each protein-binding peak (~1 to ~1kb
		wide) across the whole genome, e.g. protein
		that binds accruately to some specific motifs.
	dregion:
		analyze each protein-binding region (~1 to
		~10kb wide) across the whole genome, e.g.
		some histone modifications.
	dtriple:
		Do analysis at all three levels including each
		region, peak, and position. Would be useful
		when little is known about the potential binding
		pattern.
	profile:
		analyze wiggle format occupancy or differential
		signal profile relative to gene structures or
		bed format genomic regions.
	wiq:
		normalize wiggle files to have the same quantiles (Quantile normalization).
	wig2wiq:
		convert wiggle format file to wiq format.
	stat:
		some statistics for positions, peaks, or regions.
	selector:
		select a subset of positions, peaks, or regions
		by value ranges or gene structures neighboring.
	valuesAtRanks:
		retrieve position, peak, or region values by ranks.

Kaifu Chen, et al. chenkaifu@gmail.com, Li lab, Biostatistics department, Dan L. Duncan cancer center, Baylor College of Medicine.
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. DANPOS.sh). For example:

#!/bin/bash
set -e
module load DANPOS
danpos.py dops sampleA

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=2 --mem=2g DANPOS.sh

Create a swarmfile (e.g. DANPOS.swarm). For example:

cd dir1;danpos.py dpos sampleA
cd dir2;danpos.py dpos sampleB

Submit this job using the swarm command.

swarm -f DANPOS.swarm [-g #] [-t #] --module DANPOS