#!/bin/bash

## Modify this job script accordingly and submit with the command:
##    sbatch HPC.sbatch
#SBATCH --nodes=1   # number of nodes
#BATCH --ntasks-per-node=16   # 16 processor core(s) per node
#SBATCH --job-name='MapMiwiKO'
#SBATCH --mem=100000
#SBATCH --partition="all"
#SBATCH --mail-user=kara.stark@duke.edu   # email address
#SBATCH --mail-type=BEGIN
#SBATCH --mail-type=END
#SBATCH --mail-type=FAIL
#SBATCH --output="1-%j.out"
#SBATCH --error="1-%j.err"
## LOAD MODULES, INSERT CODE, AND RUN YOUR PROGRAMS HERE


export PATH=/data/zhanglab/Weijia_Su/software/samtools-1.12/bin:$PATH 

genome="/data/zhanglab/oliver_chung/references/mm10.fa" 

samtools merge miwi-het-barcode4-12.bam barcode12.fastqmm10.sorted.bam barcode04.fastq.fastqmm10.sorted.bam