Publication:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6707278/

PRJNA517683

#!/bin/bash
#SBATCH --time=23:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=36
#SBATCH --job-name="get1"
#SBATCH --mail-type=BEGIN
#SBATCH --mail-type=END
#SBATCH --mail-type=FAIL
#SBATCH --output=job.%J.out
#SBATCH --error=job.%J.err
#SBATCH --mail-user=mhrwoodhouse@gmail.com
#SBATCH --mail-type=BEGIN,END,FAIL

ulimit -s unlimited

module load trimgalore
module load bowtie
module load samtools
module load picard
module load bedtools2

for sample in *.fastq.gz
        do
          	echo $sample
                describer=$(echo ${sample} | sed 's/.fastq.gz//')
                echo $describer

trim_galore ${sample}

zcat ${describer}_trimmed.fq.gz > ${describer}_trimmed.fq   

bowtie -X 1000 -m 1 -v 2 --best --strata /work/LAS/mhufford-lab/mw2/epigenetics/bowtie_B73v5/B73_v5 ${describer}_trimmed.fq -S ${describer}_trimmed.sam

samtools view --threads 36 -b -o ${describer}_trimmed.bam  ${describer}_trimmed.sam
samtools sort -o ${describer}_sorted.bam -T ${sample}_temp --threads 36 ${describer}_trimmed.bam

picard MarkDuplicates I=${describer}_sorted.bam O=${describer}_removed_dups.bam M=marked_dup_metrics.txt REMOVE_DUPLICATES=true

bedtools genomecov -bg -ibam ${describer}_removed_dups.bam -split -scale 1.0 > ${describer}.bedgraph

/work/LAS/mhufford-lab/mw2/kentUtils/bin/linux.x86_64/bedGraphToBigWig ${describer}.bedgraph /work/LAS/mhufford-lab/mw2/epigenetics/B73v5.sizes ${describer}.bw

done




For merging the tassel2 and 3 reads:

#!/bin/bash
#SBATCH --time=05:00:00 
#SBATCH --nodes=1 
#SBATCH --ntasks-per-node=36
#SBATCH --job-name="merge"
#SBATCH --mail-type=BEGIN
#SBATCH --mail-type=END
#SBATCH --mail-type=FAIL
#SBATCH --output=job.%J.out
#SBATCH --error=job.%J.err 
#SBATCH --mail-user=mhrwoodhouse@gmail.com 
#SBATCH --mail-type=BEGIN,END,FAIL 

module load samtools
module load bedtools2
module load picard

For calling peaks with peakranger:

/work/LAS/mhufford-lab/mw2/epigenetics/peakranger ranger --format bam SRR8502759_removed_dups.bam SRR8502757_removed_dups.bam SRR8502759_rep2_ranger -t 15
/work/LAS/mhufford-lab/mw2/epigenetics/peakranger ranger --format bam SRR8502760_removed_dups.bam SRR8502758_removed_dups.bam SRR8502760_rep2_ranger -t 15

for calling peaks with MACS2:

macs2 callpeak -t SRR8502759_removed_dups.bam -c SRR8502757_removed_dups.bam -f BAMPE -n SRR8502759_rep2_macs2 -g 2.2e9 --keep-dup all 
macs2 callpeak -t SRR8502760_removed_dups.bam -c SRR8502758_removed_dups.bam -f BAMPE -n SRR8502760_rep1_macs2 -g 2.2e9 --keep-dup all