peiyulin/atacgraph repository overview

⁠Installation

pull the official docker image by running:

docker pull peiyulin/atacgraph

⁠Usages

To use the ATACgraph Docker container, the folder has to be mounted from the host system into the container with the -v argument. The examples mount the current working directory under /app inside the container and then run the command:

docker run --rm -v $(pwd):/app peiyulin/atacgraph:latest /ATACgraph/script/ATACgraph command /app/input /app/output 

⁠Examples

Download the demo input files

wget https://github.com/RitataLU/ATACgraph/raw/master/demo/demo.tar.gz
tar -xvf demo.tar.gz 
cd demo

⁠Preprocessing of alignment read

Remove mitochondria chromosome

Input:

• ATAC-seq bam file

docker run --rm -v $(pwd):/app peiyulin/atacgraph:latest /ATACgraph/script/ATACgraph 00_rmChr /app/demo.bam /app/demo_rmM.bam chrM

Output:

• ATAC-seq bam file after removing mitochondria chromosome: demo_rmM.bam

⁠Fragment length distribution and Fast Fourier Transform (FFT)

Input:

• Removed mitochondria ATAC-seq bam file

docker run --rm -v $(pwd):/app peiyulin/atacgraph:latest samtools index /app/demo_rmM.bam
docker run --rm -v $(pwd):/app peiyulin/atacgraph:latest /ATACgraph/script/ATACgraph 01_calFragDist /app/demo_rmM.bam /app/demo_rmM_fragment  /app/demo_rmM_FFT

Output:

• ATAC-seq bam file after removing mitochondria chromosome index: demo_rmM.bam.bai
• 2 figures: demo_rmM_fragment.png & demo_rmM_FFT.png

⁠Transform GTF file to BED files

Input:

• Annotation GTF file

docker run --rm -v $(pwd):/app peiyulin/atacgraph:latest /ATACgraph/script/ATACgraph 02_gtftoBed /app/demo_gene.gtf /app/demo -p 2000

Output:

• 11 BED file (promoter,gene,exon,intron,utr5,cds,utr3,igr) for the generating metagene plots, fold enrichment analysis

⁠ATAC-seq peak calling

Input:

• Removed mitochondria ATAC-seq bam file

docker run --rm -v $(pwd):/app peiyulin/atacgraph:latest /ATACgraph/script/ATACgraph 03_callPeak /app/demo_rmM.bam /app/demo_rmM_peakcall /app/demo_gene_body_bed6.bed

Output:

• Peak location BED file: demo_rmM_peakcall_peaks.narrowPeak
• Peak intensity bigWigfile: demo_rmM_peakcall_coverage.bw
• A genes list of overlapping with peaks locations: demo_rmM_peakcall_peak_gene_list.txt

⁠Visualisasion

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:

• Removed mitochondria ATAC-seq bam file

docker run --rm -v $(pwd):/app peiyulin/atacgraph:latest /ATACgraph/script/ATACgraph 03_genePlot /app/demo_rmM_peakcall.narrowpeak /app/demo_rmM_peakcall_coverage.bw /app/demo 

Output:

3 Figures

• The enrichment status of the accessible region in the genome: demo_rmM_peakcall_Fold_Enrichment.pdf
• The accessibility – or read abundance – around genes: demo_rmM_peakcall_gene_body_heatmap.pdf
• The accessibility – or read abundance – around pthe eaks: demo_rmM_peakcall_Peak_heatmap.pdf

text files

• value of Heatmap depicting accessibility for gene: demo_rmM_peakcall_coverage.bwgene_body.matrix.txt & demo_rmM_peakcall_coverage.bwgene_body.matrix.gz
• value of Heatmap depicting accessibility for peak: demo_rmM_peakcall_coverage.bw_peak.matrix.txt & demo_rmM_peakcall_coverage.bw_peak.matrix.gz
• The value to generate the enrichment figure: demo_rmM_peakcall_peaks.narrowPeak_Fole_Enrichment_Table.txt
• The intersection site between 8 genomic features and peaks