#!/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" 

for barcode in /data/zhanglab/Kara_Stark/Kara_data/20221013_pico-seq_miwi_4C/fastq_pass/barcode*;
do
barcode_name=$(basename $barcode)
cat $barcode"/"*".fastq" > "/data/zhanglab/Kara_Stark/Kara_data/20221013_pico-seq_miwi_4C/fastq_pass/"$barcode_name".fastq";
done

for file in /data/zhanglab/Kara_Stark/Kara_data/20221013_pico-seq_miwi_4C/fastq_pass/*.fastq; 
do 
name=$(basename $file)
/data/zhanglab/oliver_chung/software/minimap2/minimap2 -ax map-ont $genome $file > $name"mm10.sam"; 
samtools view -S -b $name"mm10.sam" > $name"mm10.bam";
samtools sort $name"mm10.bam" -o $name"mm10.sorted.bam";
samtools index $name"mm10.sorted.bam";
/data/zhanglab/oliver_chung/software/anaconda3/bin/bamCoverage -b $name"mm10.sorted.bam" -o $name"mm10.sorted.bw";
done