Source:
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https://yiweiniu.github.io/blog/2019/03/ATAC-seq-data-analysis-from-FASTQ-to-peaks/
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https://informatics.fas.harvard.edu/atac-seq-guidelines.html
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You will need Genrich (if using Genrich for peack-calling) and MSPS if mergeing peacks.
module add sratoolkit
module add trim-galore/0.6.7
module add bowtie2
module add samtools
module add sambamba
module add macs3
f=<fastq filename prefix> # e.g. SRA ID . If slow, download from ENA
p=64 #number of processors
ind=/mm10/mm10 # bowtie2 index path to .bt files
fasterq-dump $f -p "-e$p"
trim_galore -q 0 --length 0 "$f".fastq -j $p
bowtie2 -q -x $index -U "$f"_trimmed.fq -S $f.sam --local --no-unal --very-sensitive -p $p
samtools view $f.sam -b > $f.bam -@ $p
samtools view -q 30 $f.bam -b -h > $f.p.bam -@ $p
samtools sort $f.p.bam > "$f".s.bam -@ 16
java -Xmx120g -jar picard.jar MarkDuplicates I=$f.s.bam O=$f.pic.bam M=tmp REMOVE_DUPLICATES=true
macs3 callpeak -t $f.pic.bam -g hs -n $f.bed -q 0.01 --broad
module add sratoolkit
module add trim-galore/0.6.7
module add bowtie2
module add samtools
module add sambamba
module add macs3
f=<fastq filename prefix> # e.g. SRA ID
p=64 #number of processors
ind=/mm10/mm10 # bowtie2 index path to .bt files
fasterq-dump $f -p "-e$p"
trim_galore --paired -q 0 --length 0 "$f"_1.fastq "$f"_2.fastq -j $p
bowtie2 -q -x $ind -1 "$f"_1_val_1.fq -2 "$f"_2_val_2.fq -S $f.sam --local --no-unal --very-sensitive -X 2000 -p $p
samtools view $f.sam -b > $f.bam -@ $p
samtools view -q 30 $f.bam -b -h > $f.q.bam -@ $p
samtools view -F 1804 $f.q.bam -b -h > $f.qq.bam -@ $p
samtools view -f 2 $f.qq.bam -b -h > $f.p.bam -@ $p #proper paired
samtools sort $f.p.bam > "$f".s.bam -@ 16
java -Xmx120g -jar picard.jar MarkDuplicates I=$f.s.bam O=$f.pic.bam M=tmp REMOVE_DUPLICATES=true
macs3 callpeak -f BAMPE -t $f.pic.bam -g hs -n $f.bed -q 0.01 --broad
samtools sort -n $f.bam > "$f"_n.bam -@ 16
Genrich -t "$f"_n.bam -o $f.bed -j -y -r -e chrM -v
bedtools intersect -v -a $f.bed_peaks.broadPeak -b mm10-blacklist.v2.bed > $f.bed
mspc -i *.bed -r bio -w 1e-4 -s 1e-8
bedops -i *Peak > int.bed
bedtools coverage -a int.bed -b $f/$f.pic.bam > $f.cov