ATAC-seq-Pipeline/05_bedCount.sh at main · Alghurmff/ATAC-seq-Pipeline · GitHub

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#!/bin/bash
#SBATCH --partition=%partition%
#SBATCH --nodes=%nodes%
#SBATCH --cpus-per-task=20
#SBATCH --job-name=%jobname%
#SBATCH --output=%outputlog%
#SBATCH --error=%errorlog%
#SBATCH --mail-user=%mail%
#SBATCH --mail-type=FAIL
#SBATCH --time=24:00:00
#SBATCH --mem=%mem%

#slurm configuration
partition="batch"
mem="100G"
nodes="1"
mail="YOUR EMAIL"
jobname=bedCount
outputlog=${Out_Dir}/bedCount.out
errorlog=${Out_Dir}/bedCount.err

#***********************************#
# ATAC-Seq pipeline - PAIR-END      #
# script: 10_bedCount.sh            #
#***********************************#


module load bedtools/2.29.0

# 10. Count the number of reads mapping to each feature (OCR)

# for all cell types:
filenames=$(ls /ibex/alghurmf/bulkAtac/*/04bam/*.clean.bam | grep "HSC\|CLP\|proB\|preB\|PreProB\|ImmatureB\|neutrophils")
bed_file="bulkAtac/BedCount/Allconsensus_cell_types.bed"

Out_Dir="bulkAtac/BedCount"   # path of output folder

bedtools multicov -bams $filenames -bed $bed_file  -D > $Out_Dir/count_table.txt