nucwave.rst

NUCwave

NUCwave is a wavelet-based bioinformatic tool that generates nucleosome occupation maps from sequence reads generated by:

Chromatin digestion with micrococcal nuclease (MNase-seq)

Chemical cleavage of chromatin (CC-seq)

Chromatin inmunoprecipitation (ChIP-seq) and fragmentation by sonication

NUCwave can process datasets by sequencing protocols:

Single-read (SR)

Paired-end (PE)

NUCwave requires only two inputs:

The dataset of aligned sequence reads

The sequence of the reference genome

NUCwave is implemented in Python and is distributed under GPLv3 license.

If you use NUCwave, please cite :

Comparative analysis of methods for genome-wide nucleosome cartography . Luis Quintales, Enrique Vázquez and Francisco Antequera (2015) Briefings in Bioinformatics 16: 576-587

Download

Source Code

Dependencies:

Python3

numpy

PyWavelets

Manual

nucwave_sr.py

Direct generation of nucleosome maps from single-read MNase-seq, ChIP-seq, and CC-seq (chemical cleavage) experiments. For chemical cleavage experiments -c option must be used. Paired-end experiments can also be analyzed as single-read.

$ python nucwave_sr.py -h
        usage: python nucwave_sr.py [-h] [-w] [-c] [-o OUTDIR] -g GENOMEFILE -a

ALIGNFILE -p PREFIXNAME
optional arguments:

-h, --help

show this help message and exit

-w, --wigfiles

write intermediate wig files

-c, --chemical

chemical cleavage

-o OUTDIR

output directory

-g GENOMEFILE

FASTA genome file

-a ALIGNFILE

BOWTIE alignment file

-p PREFIXNAME

Prefix name for result files

Alignment file format

Each line of the input alignment file must contain 4 fields separated by a tab character:

strand chromosome genomic_coordinate sequence

nucwave_pe.py

Direct generation of nucleosome maps from paired-end MNase-seq, ChIP-seq, and CC-seq (chemical cleavage) experiments. For chemical cleavage experiments, this program generates a map of linker positions.

optional arguments:

-h, --help: show this help message and exit
-w, --wigfiles: write intermediate wig files
-o OUTDIR: output directory

required arguments: