GridTools

GridTools is a set of tools designed for analyzing GRID-seq data that genome-wide captures RNA-chromatin interactions.

Install

GridTools is developed in Python 3.6.4 and compatible with Python 3.6+, with dependent libraries as below:

Requirements

We recommend using conda package manager (https://conda.io/miniconda.html) to install required bioinformatics tools and packages in Bioconda (https://bioconda.github.io/). And install bwa, samtools, cutadapt, numpy, scipy, pandas, pysam, h5py:

conda install -c bioconda bwa samtools cutadapt numpy scipy pandas pysam h5py

Installing

GridTools is ready to use without any further setups in install.

cp gridtools/GridTools.py ~/bin
chmod +x ~/bin/GridTools.py

Usage

GridTools.py [-h] [--version] {matefq,evaluate RNA,DNA,matrix,model,stats} ...

There are 7 sub-commands designed for specific functions.

sub-command	function
matefq	parse BAM file that mapped to GRID-seq linker to RNA-DNA mate in interleaved FASTQ file.
evaluate	evaluate the RNA-DNA mates quality and quanitity from the BAM file mapped to the genome.
RNA	identify chromatin-enriched RNAs.
DNA	identify RNA-enriched chromatin regions in background (trans) and foreground (cis).
matrix	cacluate the RNA-chromatin interation matrix.
model	model the network of enhancer-promoter proximity.
stats	statistics of GRID-seq data.

matefq

GridTools.py matefq [-h] -o HDF5 [-l MINLEN] [-n READNAME] bam

parse BAM file that mapped to GRID-seq linker to RNA-DNA mate in interleaved FASTQ file.

arguments	option	description
`bam`	required	BAM file mapped to the GRID-seq Linker.
`-o/--hdf5 HDF5`	required	output mapping information to HDF5.
`-l/--minlen MINLEN`	optional	filter RNA-DNA mates with both RNA and DNA length >= MINLEN [default: 19].
`-n/--readname READNAME`	optional	rename the prefix of each read [default: no change].

evaluate

GridTools.py matefq [-h] -o HDF5 [-k BINK] [-m WINM] -g GTF bam

evaluate the RNA-DNA mates quality and quanitity from the BAM file mapped to the genome.

arguments	option	description
`bam`	required	BAM file mapped to the GRID-seq Linker.
`-o/--hdf5 HDF5`	required	output mapping information to HDF5.
`-g/--gtf GTF`	required	gene annotation in GTF format.
`-k/--bink BINK`	optional	bin size (kb) of the genome [default: 10 kb].
`-m/--winm WINM`	optional	moving window for smoothing in bins [default: 10].

RNA

GridTools.py RNA [-h] [-e EXPRS] [-s SCOPE] hdf5

identify chromatin-enriched RNAs and evaluate the gene expressoin levels as well as interaction scopes.

arguments	option	description
`hdf5`	required	HDF5 file with mapping information evaluated by GridTools.
`-e/--exprs EXPRS`	optional	output file for the gene expression [default: print to the screen].
`-s/--scope SCOPE`	optional	output file for the RNA interaction scope [default: None].

DNA

GridTools.py DNA [-h] hdf5

identify RNA-enriched chromatin regions in background (trans) and foreground (cis).

arguments	option	description
`hdf5`	required	HDF5 file with mapping information evaluated by GridTools.

stats

GridTools.py stats [-h] -p PREFIX [-b] [-c] [-l] [-r] hdf5

statistics of GRID-seq data.

arguments	option	description
`hdf5`	required	HDF5 file with mapping information evaluated by GridTools.
`-p/--prefix PREFIX`	required	prefix of output file names.
`-b/--bases`	optional	if output the summary of base-position information for RNA, Linker and DNA [default: No].
`-c/--counts`	optional	if output the summary of mapping information in read counts [default: No].
`-l/--lengths`	optional	if output the distribution of sequence length for RNA, Linker and DNA [default: No].
`-r/--resolution`	optional	if output the resolution information of the library [default: No].

matrix

GridTools.py matrix [-h] [-k RPK] [-x DRPK] hdf5

cacluate the RNA-chromatin interation matrix.

arguments	option	description
`hdf5`	required	HDF5 file with mapping information evaluated by GridTools.
`-k/--rpk RPK`	optional	cutoff of RNA reads per kilobase in the gene body. [default: 100]
`-x/--drpk DRPK`	optional	cutoff of DNA reads per kilobase at the maximum bin [default: 10].

model

GridTools.py model [-h] [-k RPK] [-x DRPK] -e ELEBED [-z ZSCORE] hdf5

model the network of enhancer-promoter proximity.

arguments	option	description
`hdf5`	required	HDF5 file with mapping information evaluated by GridTools.
`-e/--elebed ELEBED`	required	BED file of regulatory elements (eg. enhancers and promoters).
`-k/--rpk RPK`	optional	cutoff of RNA reads per kilobase in the gene body. [default: 100]
`-x/--drpk DRPK`	optional	cutoff of DNA reads per kilobase at the maximum bin [default: 10].
`-z/--zscore ZSCORE`	optional	z-score to filter the significant proximity [default:-10].

Simple Code Example

The test data and demo code for the GRID-seq analysis with test dataset at: http://fugenome.ucsd.edu/gridseq/datasets/gridseq.test10M.raw.fq.gz:

Demo code is in the gridtools/pipeline/Snakefile.py

License

The GridTools is licensed under MIT. The detailed license terms are in the LICENSE file.

zhouyu/gridtools