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https://github.com/RitataLU/ATACgraph
https://github.com/RitataLU/ATACgraph
Last synced: about 1 month ago
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- Host: GitHub
- URL: https://github.com/RitataLU/ATACgraph
- Owner: RitataLU
- License: gpl-3.0
- Created: 2019-06-17T04:16:26.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2023-01-18T19:18:44.000Z (over 1 year ago)
- Last Synced: 2024-02-12T23:48:25.707Z (5 months ago)
- Language: Python
- Size: 40.8 MB
- Stars: 16
- Watchers: 0
- Forks: 5
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Lists
- awesome-atac-analysis - ATACgraph
README
# ATACgraph
ATACgraph is a simple and effective software for the analysis of ATAC-Seq data. It contains 12 analyses to profile (epi)genome.
# Citations
If you use ATACgraph for your analysis, please cite it using the following [manuscript](https://pubmed.ncbi.nlm.nih.gov/33584814/)
```
Lu RJ, Liu YT, Huang CW, Yen MR, Lin CY, Chen PY.
ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq. Front Genet. 2021 Jan 13;11:618478.
https://www.frontiersin.org/articles/10.3389/fgene.2020.618478/full
PMID: 33584814
```
# ATACgraph Pipeline
# System Requirements
* Linux or Mac OS Environment
* Python 2.7
* deepTools 3.3.0
* [BEDtools](http://bedtools.readthedocs.org/)
* [IDR](https://github.com/nboley/idr)
```
IDR require python 3.5
```
* [MACS2](https://github.com/taoliu/MACS)
* Python Modules:
* Numpy
* pandas
* pysam==0.11.2.2
* matplotlib
* matplotlib-venn
* argparse
* pybedtools
* deepTools==3.3.0
* scikit-learn
# Tutorial
Please follow the tutorial of example use case
* [Tutorial](https://github.com/RitataLU/ATACgraph/blob/master/Tutorial.md)
# Installation
## Docker version
* [ATACgraph Galaxy](https://hub.docker.com/r/lsbnb/galaxy_atacgraph)
## Linux Command Version
1. Download the source code and install the requirements.
```
$ git clone https://github.com/RitataLU/ATACgraph.git
$ cd ATACgraph
$ sudo sh ./base.txt
```
2. Add your ATACgraph path to the PATH.
(1) Edit bash profile
```
$ vi ~/.bash_profile
```
(2) Add ATAC-graph/script path to the PATH environment variable.
```
$ PATH=$PATH:(ATACgraph/script file path)
$ source ~/.bash_profile
```
# Running ATACgraph
## Filtering reads overlapped with blacklist region
Users can filter reads by this command before running ATACgraph if they have a blacklist.
```
bedtools intersect -v -abam input.bam -b hg19_blacklist.bed > output.bam
```
## ATACgraph modules
```
$ ATACgraph -h
Usage: atacG [options]
ATACgraph sub-commands include:
00_rmChr Remove chrM,chrPt
01_calFragDist Generate figures of fragments size distribution & Fast Fourier transform
02_selectFragSize Select bam fragments size
02_gtftoBed Transform gtf file to bed files
03_callPeak Call ATAC-seq peaks"
03_genePlot Generate figures of depicting genes and peaks accessibility
03_junctionBed Generate junction bed track
04_specificPeaks Identify specific peaks between 2 groups of peaks
04_specificPeaksIDR Identify specific peaks with Irreproducibility Discovery Rate (IDR) framework
04_specificPromoter Identify specific promoter using Gaussian Mixture Model between 2 groups of peaks
05_seqCompare Compare peaks between ATAC-seq and Other seq
05_compareToRNA Comparison of accessible genes and genes expression
```
## Filtering ATAC-seq reads from any chromosome
**Input:**
* ATAC-seq reads file in bam
```
$ ATACgraph 00_rmChr -h
Usage: 00_rmChr
If you need to remove multiple chromosomes, use comma
to seperate. For example chrM,chrPt
```
**Output:**
* ATAC-seq bam file after removing mitochondria chromosome
## Fragment length distribution and Fast Fourier Transform (FFT)
**Input:**
* ATAC-seq bam file after removing mitochondria chromosome
```
$ ATACgraph 01_calFragDist -h
usage: 01_calFragDist [-h] input_bam fragment_distribution_outname
fragment_fft_outname
positional arguments:
input_bam
fragment_distribution_outname
fragment_fft_outname
optional arguments:
-h, --help show this help message and exit
```
**Output:**
* 2 figures (fragment lenth distribution & FFT analysis result)
* fragment distribution
* fragment distribution FFT
**Output:**
* filtered bam file
## Selectiing fragments size
**Input:**
* ATAC-seq reads file in bam
```
$ ATACgraph 02_selectFragSize -h
usage: 02_selectFragSize [-h] [-f FILTER] [-m MODE] input_bam output_bam
positional arguments:
input_bam
output_bam
optional arguments:
-h, --help show this help message and exit
-f FILTER, --filter FILTER
default=150
-m MODE, --mode MODE Select fragments smaller [1] or larger [2] than filter
size. Default=1
```
**Output:**
* fragment bam file
## Transform GTF file to BED files
**Input:**
* ATAC-seq bam file after removing mitochondria chromosome
```
$ ATACgraph 02_gtftoBed -h
usage: gtftoBed [-h] [-p PROMOTER] input_gtf gtf_name
positional arguments:
input_gtf
gtf_name
optional arguments:
-h, --help show this help message and exit
-p PROMOTER, --promoter PROMOTER, promoter region from gene transcript start site (TSS) default = 2000
```
**Output:**
* 11 BED file (promoter,gene,exon,intron,utr5,cds,utr3,igr) for the generating metagene plots, fold enrichment analysis
## Generating fragment size tracks
**Input:**
* ATAC-seq bam file after removing mitochondria chromosome
```
ATACgraph 03_junctionBed -h
usage: junctionBed [-h] [-s SEPARATE] [-b BIN] [-f FILTER]
input_bam output_bed
positional arguments:
input_bam
output_bed
optional arguments:
-h, --help show this help message and exit:w
-s SEPARATE, --separate SEPARATE
border lenth of long and short fragment(bp), default: 150
-b BIN, --bin BIN binzise of genome(bp), default: 10
-f FILTER, --filter FILTER
number of fragment juction tracks, default:1
```
**Output:**
* track BED files
* Visualization on IGV
## ATAC-seq peak calling
**Input:**
* ATAC-seq bam file
```
ATACgraph 03_callPeak -h
usage: 03_callPeak.py [-h] [-s SEPARATE] [-shift SHIFT] [-ES EXTEND]
[-bs BINSIZE] [-c CONTROL_BAM]
input_bam output_name gene_bed
positional arguments:
input_bam input ATAC-seq bam file
output_name name for output files
gene_bed Gene or promoter annotation bed file, either
gene_body_bed6.bed or gene_promoter_bed6.bed
optional arguments:
-h, --help show this help message and exit
-s SEPARATE 1: integration site; 2: full-extend fragment
-shift SHIFT shift size from integration site(bp), default: 50
-ES EXTEND extend size from integration site (bp), default: 100
-bs BINSIZE bin size for bigwig (bp), default: 10
-c CONTROL_BAM input control bam file, default: none
```
**Output:**
* Peak location BED file (.narrowpeak),
* Peak intensity bigWigfile (.coverage.bw)
* A genes list of overlapping with peaks locations (.peak_gene_list.txt)
## Identify differential enriched ATAC-seq peaks between two conditions.
To identify differentially accessible regions, ATACgraph utilizes peak BED files and BigWig files generated by callPeak module to compute peaks abundances between two samples.
**Input:**
* 2 ATAC-seq peaks BDE files
* 2 ATAC-seq abundandance BigWig files
```
ATACgraph 04_specificPeaks -h
usage: specificPeaks [-h] [-c FOLD_CHANGE] [-p P_VALUE] input_peakAs input_peakBs input_bwAs input_bwBs output_bedA output_bedB
positional arguments:
input_peakAs Peak beds, seprate by comma
input_peakBs Peak beds, seprate by comma
input_bwAs BigWig files, seprate by comma
input_bwBs BigWig files, seprate by comma
output_bedA
output_bedB
optional arguments:
-h, --help show this help message and exit
-c FOLD_CHANGE, --fold_change FOLD_CHANGE
Fold change cutoff. Default:2
-p P_VALUE, --p_value P_VALUE
P-value cutoff. Default:0.05
```
**Output:**
* 2 ATAC-seq specific peaks BED files
## Identify differential enriched ATAC-seq peaks between two conditions with IDR
```
idr --samples 1. narrowPeak 2.narrowPeak --output-file idr.txt
```
**Output:**
* A txt files, format information are based on [IDR](https://github.com/nboley/idr)
```
ATACgraph 04_specificPeaks -h
usage: specificPeaks [-h] [-c FOLD_CHANGE] [-p P_VALUE] input_peakAs input_peakBs output_bedA output_bedB
positional arguments:
input_peakAs Peak beds, seprate by comma
input_peakBs Peak beds, seprate by comma
output_bedA
output_bedB
optional arguments:
-h, --help show this help message and exit
```
**Output:**
* 2 ATAC-seq specific peaks BED files
## Comparing peaks between ATAC-seq and another Seq.
**Input:**
* ATAC-seq peaks BED file & another seq peaks file
```
ATACgraph 05_seqCompare -h
usage: seqCompare [-h] atac_peak other_peak ATAC_name otherPeak_name overlap_name Genome_size genes
positional arguments:
atac_peak ATAC-seq peak bed
other_peak Other seq peak bed
ATAC_name Name for ATAC peak
otherPeak_name Name for other peak
overlap_name Name for overlapping peak
Genome_size Genome size(bp)
genes Gene or promoter annotation file with bed6.bed format
optional arguments:
-h, --help show this help message and exit
```
**Output:**
* An overlapping peaks location BED file
* Venn diagram shows the numbers of each seq peaks and over lapping peaks with p value (hypergeometric test)
* A gene list of overlapping peaks locations between 2 seq
## Comparing peaks between ATAC-seq and RNA-Seq.
**Input:**
* ATAC-seq peak containing genes in BED file & Gene expression table
```
ATACgraph 05_compareRNA -h
sage: 05_compareRNA.py [-h] [-b BINS] atac_gene RNA_seq outVenn outBar
positional arguments:
atac_gene ATAC-seq peak containing genes in bed
RNA_seq Expression table
outVenn Venn diagram output file name
outBar Barplot output file name
optional arguments:
-h, --help show this help message and exit
-b BINS, --bins BINS Number of bins; default 10
```
**Output:**
* A barplot shows percentage of accessible genes in each expression group.
* Venn diagram shows the overlapping genes between accessible regions and highly or lowly expression genes
## Heatmap and metagene plots of ATAC-seq abundance, Fold enrichment analysis of open regions in genomic features
To investigate the chromatin accessibility around genes, To investigate the chromatin accessibility around genes, ATACgraph uses the files describing the ATAC-seq peak locations and gene annotations for two types of analyse. This step requires 8 genomic feature BED files, user should run gtftoBed before this step.
**Input:**
* ATAC-seq bam file
```
ATACgraph 03_genePlot -h
usage: genePlot [-h] [-p PROMOTER] input_peak input_bigwig gtf_name
positional arguments:
input_peak
input_bigwig
gtf_name
optional arguments:
-h, --help show this help message and exit
-p PROMOTER, --promoter PROMOTER
```
**Output:**
* 3 Figures
* The enrichment status of accessible region in genome (Fold_Enrichment.pdf)
* The accessibility – or read abundance – around genes (gene_body_heatmap.pdf)
* The accessibility – or read abundance – around peaks (Peak_heatmap.pdf)
* text files
* The value of Heatmap depicting accessibility for gene (genebody.matrix.txt & genebody.matrix.gz)
* The value of Heatmap depicting accessibility for peak (peak.matrix.txt & peak.matrix.gz)
* The intersection site between 8 genomic features and peaks (8 files)
* peakcall_peaks.narrowPeak_3utr.txt
* peakcall_peaks.narrowPeak_exons.txt
* peakcall_peaks.narrowPeak_gene_igr.txt
* peakcall_peaks.narrowPeak_5utr.txt
* peakcall_peaks.narrowPeak_gene_promoter.txt
* peakcall_peaks.narrowPeak_cds.txt
* peakcall_peaks.narrowPeak_gene_body.txt
* peakcall_peaks.narrowPeak_introns.txt
* Figures
* Fold enrichment analysis of open regions in genomic features (.Fold_Enrichment.png)
* heatmap, metaplot ATAC-seq abundance related to genes
* heatmap, metaplot ATAC-seq abundance related toand peaks
