ATAC-seq | TOBIAS | footprint分析

 

The ENCODE Blacklist: Identification of Problematic Regions of the Genome
https://github.com/Boyle-Lab/Blacklist/tree/master

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
https://www.nature.com/articles/s41467-020-18035-1#Abs1

https://github.com/loosolab/TOBIAS

conda activate cutrun
pip install tobias

　　

### parameter
genome=/home/zz950/reference/refdata-gex-GRCh38-2020-A/fasta/genome.fa
blacklist=/home/zz950/reference/hg38-blacklist.v2.bed
bed=/home/zz950/projects/BAF_SOX9/diffbind/keyRdata/all.ATAC.234648.peaks.bed

### create folders
out_dir_qc=0.fastqc_report
out_dir1=1.clean_fastq
# out_dir2=2.Ecoli_bam
out_dir3=3.bam
out_dir4=4.frag
out_dir5=5.bigwig
out_dir6=6.peak # do it in another script
out_dir7=7.footprinting

mkdir $out_dir7

# ######################### main loop #############################
cat $SampleCSV | while IFS="," read sample fq1 fq2; do
###################################################################

#
/home/zz950/softwares/miniconda3/envs/cutrun/bin/TOBIAS ATACorrect --bam $out_dir3/${sample}.sorted.mapped.bam \
                                --genome $genome \
                                --peaks $bed \
                                --blacklist $blacklist \
                                --outdir $out_dir7 \
                                --cores 20

/home/zz950/softwares/miniconda3/envs/cutrun/bin/TOBIAS FootprintScores --signal $out_dir7/${sample}.sorted.mapped_corrected.bw \
                                --regions $bed \
                                --output $out_dir7/${sample}_footprints.bw \
                                --cores 20

 

# filter peaks
# grep 'chr' /home/zz950/projects/BAF_SOX9/diffbind/keyRdata/all.ATAC.234648.peaks.bed > all.ATAC.234648.peaks.bed

genome=/home/zz950/reference/refdata-gex-GRCh38-2020-A/fasta/genome.fa
blacklist=/home/zz950/reference/hg38-blacklist.v2.bed
bed=/home/zz950/projects/BAF_SOX9/diffbind/keyRdata/all.ATAC.234648.peaks.bed
motif=/home/zz950/reference/JASPAR2024_CORE_vertebrates_non-redundant_pfms_jaspar.txt

/home/zz950/softwares/miniconda3/envs/cutrun/bin/TOBIAS BINDetect --motifs $motif \
				--signals DMSO_1_footprints.bw D4_1_footprints.bw \
				--genome $genome \
				--peaks $bed \

				--outdir BINDetect_output \
				--cond_names DMSO_1 D4_1 \
				--cores 20
# 				# --peak_header test_data/merged_peaks_annotated_header.txt \

　　

TOBIAS PlotAggregate --TFBS BINDetect_output/SOX9_MA0077.2/beds/SOX9_MA0077.2_all.bed  --signals DMSO_1_footprints.bw D4_1_footprints.bw --output SOX9_footprint_comparison.pdf --share_y both --plot_boundaries --signal-on-x --flank 70

TOBIAS PlotAggregate --TFBS BINDetect_output/SOX8_MA0868.3/beds/SOX8_MA0868.3_all.bed  --signals DMSO_1_footprints.bw D4_1_footprints.bw --output SOX8_footprint_comparison.pdf --share_y both --plot_boundaries --signal-on-x --flank 70

TOBIAS PlotAggregate --TFBS BINDetect_output/BATF_MA1634.2/beds/BATF_MA1634.2_all.bed  --signals DMSO_1_footprints.bw D4_1_footprints.bw --output BATF_footprint_comparison.pdf --share_y both --plot_boundaries --signal-on-x --flank 70

TOBIAS PlotAggregate --TFBS BINDetect_output/JUND_MA0491.3/beds/JUND_MA0491.3_all.bed  --signals DMSO_1_footprints.bw D4_1_footprints.bw --output JUND_1_footprint_comparison.pdf --share_y both --plot_boundaries --signal-on-x --flank 70

　　

参考：/home/zz950/projects/BAF_SOX9/data/atac_pipeline