#!/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='HeLa-RNA-seq-UCSC'
#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

module load samtools

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

genome="/data/zhanglab/Kara_Stark/Kara_data/20230718_Hela-Mtx-RNA-seq/HeLa-RNA-seq-UCSC/hg38.fa"
                                                          
for file in /data/zhanglab/Kara_Stark/Kara_data/20230718_Hela-Mtx-RNA-seq/HeLa-RNA-seq-UCSC/*.sam
do
name=$(basename $file)
samtools view -S -b $name > $name".bam";
samtools sort $name".bam" -o $name".sorted.bam";
samtools index $name".sorted.bam";
/data/zhanglab/oliver_chung/software/anaconda3/bin/bamCoverage -b $name".sorted.bam" -o $name".sorted.bw";
done