for item in 52 53 54; do {
# 	mkdir "/dreamworld/ngs_data/Mariya_NGS_data_2022_08_22/Results/${item}";
# 	cd "/dreamworld/ngs_data/Mariya_NGS_data_2022_08_22/Results/${item}";
# 	cutadapt -j 20 -e 0.2 -m 8 -a "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA" -A "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT" -o "/dreamworld/ngs_data/Mariya_NGS_data_2022_08_22/Results/${item}/adless_R1.fastq.gz" -p "/dreamworld/ngs_data/Mariya_NGS_data_2022_08_22/Results/${item}/adless_R2.fastq.gz" "/dreamworld/ngs_data/Mariya_NGS_data_2022_08_22/Source/${item}_S${item}_L001_R1_001.fastq.gz" "/dreamworld/ngs_data/Mariya_NGS_data_2022_08_22/Source/${item}_S${item}_L001_R2_001.fastq.gz" > "/dreamworld/ngs_data/Mariya_NGS_data_2022_08_22/Results/${item}/cutadapt_stats.txt";
# 	bwa mem -R "@RG\tID:0\tPL:ILLUMINA\tPU:0\tLB:001\tSM:P${item}" -t 20 -v 1 "/dreamworld/databases/hg19_canonical/hg19_canonical.fa" "/dreamworld/ngs_data/Mariya_NGS_data_2022_08_22/Results/${item}/adless_R1.fastq.gz" "/dreamworld/ngs_data/Mariya_NGS_data_2022_08_22/Results/${item}/adless_R2.fastq.gz" | gatk SortSam --VERBOSITY ERROR -SO coordinate -I "/dev/stdin" -O "/dreamworld/ngs_data/Mariya_NGS_data_2022_08_22/Results/${item}/${item}.bam";
# 	gatk BuildBamIndex -I "/dreamworld/ngs_data/Mariya_NGS_data_2022_08_22/Results/${item}/${item}.bam";
	bamCoverage -b "/dreamworld/ngs_data/Mariya_NGS_data_2022_08_22/Results/${item}/${item}.bam" -o "/dreamworld/ngs_data/Mariya_NGS_data_2022_08_22/Results/${item}/${item}.coverage.bigWig";
} done
