DISPbind: Disorder protein genomic binding analysis toolkit for DisP-seq

A schematic overview of DisP-seq

Features

• Genome mapping and bigwig generation of DisP-seq sequences
• Identification of DisP island

Prerequisites

• numpy (https://numpy.org/)
• pysam (https://pysam.readthedocs.io/en/latest/api.html
• pybedtools (https://daler.github.io/pybedtools/)
• pandas (https://pandas.pydata.org/)
• pyBigWig (https://github.com/deeptools/pyBigWig)
• docopt (http://docopt.org/)
• matplotlib (https://matplotlib.org/)
• seaborn (https://seaborn.pydata.org/)
• MACS (https://github.com/macs3-project/MACS)

Installation

Install by using pip

pip install DISPbind

Usage and example

---

Step1: Genome mapping and bigwig generation of DisP-seq sequences

Usage: DISPbind align [options] -i INDEX -a FQ1 -b FQ2 -o OUT -n NAME

Options:
    -h --help                      Show help message.
    -v --version                   Show version.
    -i INDEX --index=INDEX         Index files for BWA
    -p THREAD --thread=THREAD      Running threads. [default: 10]
    -m MQ --mquality=MQUALITY      Mapping quality. [default: 10]
    -g GSIZE --gsize=GSIZE         Genome size file.
    -n NAME --name=NAME            Output file name. [default: bwa_out]
    -a FQ1 --fastq1=FQ1            Input R1 file.
    -b FQ2 --fastq2=FQ2            Input R2 file.
    -o OUT --output=OUT            Output directory. [default: alignment]

DISPbind align -i bwa_index_hg19/hg19.fa -n test -a test_file/test_SKNMC_bisox_rep_R1.fastq -b test_file/test_SKNMC_bisox_rep_R2.fastq -o test_out -p 1 -g hg19.chrom.sizes

Transfer Bam file to bigwig file (Only if you do not run the align step and could provide DisP-seq Bam file)

Usage: DISPbind bam2bw [options] -b bam -n NAME -o OUT

Options:
    -h --help                      Show help message.
    -v --version                   Show version.
    -m MQ --mquality=MQUALITY      Mapping quality. [default: 10]
    -g GSIZE --gsize=GSIZE         Genome size file.
    -n NAME --name=NAME            Output file name. [default: bwa_out]
    -b BAM --bam=BAM               Input BAM file.
    -o OUT --output=OUT            Output directory. [default: alignment]

DISPbind bam2bw -b test/test.bam -n test -o test_out -g hg19.chrom.sizes

Step2: DisP-seq peak calling by MACS

macs2 callpeak --nomodel -B --SPMR -f BAMPE -g hs -t Bisox.sorted.deduped.bam -c Input.sorted.deduped.bam --outdir callpeak/ -n bisox_peaks --broad

Step3: Identify DisP islands from bigwig and peak file

Usage: DISPbind island [options] -p PEAK (-b BW | -l LIST) -o OUT

Options:
    -h --help                             Show help message.
    -v --version                          Show version.
    -p PEAK --peak=PEAK                   DisP peaks.
    -b BW --bigwig=BW                     Bigwig file for corresponding sample.
    -o OUTPREFIX --output=OUTPREFIX       Output island file. [default: DisP]
    -l LIST --list=LIST                   Bigwig replicate (will calculate average signals for replicates)
    --plot                                Hockey plot for signal vs rank.

DISPbind island -o DisP_island.txt -p bisox_peaks.bed -b bisox.sorted.fragments.bw --plot

Format of output DisP_island.txt:

Field	Description
Chrom	Chromosome
Start	Start of DisP merged region
End	End of DisP merged region
Signal	Sum of DisP signal in merged region
Rank	Rank of DisP signal
Island	Label Island or not Island

Citation

Yu-Hang Xing*, Rui Dong*, Lukuo Lee, Shruthi Rengarajan, Nicolò Riggi, Gaylor Boulay and Miguel N. Rivera#. DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins, 2023, Nature Biotechnol

License

Copyright (C) 2022 Rivera Lab. See LICENSE for license rights and limitations (MIT).