conda activate rnaseq

bowtie2-build -f GCF_019923935.1_NDDB_SH_1_genomic.fna NCBIbuf
#####trim_galore
for i in "liver1" "liver2" "liver3" "liver4"
do
trim_galore --paired -o /public/home/dk_dyf/songxinhui/ATAC-seq/liver/02trim \
/public/home/dk_dyf/songxinhui/ATAC-seq/01data/${i}/${i}_1.fq.gz \
/public/home/dk_dyf/songxinhui/ATAC-seq/01data/${i}/${i}_2.fq.gz --fastqc  
done

#####bowtie2
for i in "liver1" "liver2" "liver3" "liver4"
do
bowtie2 -p 60 --very-sensitive -X 1000 -x /public/home/dk_dyf/songxinhui/ATAC-seq/00ref/NCBIbuf \
 -1 /public/home/dk_dyf/songxinhui/ATAC-seq/liver/02trim/${i}_1_val_1.fq.gz \
 -2 /public/home/dk_dyf/songxinhui/ATAC-seq/liver/02trim/${i}_2_val_2.fq.gz | samtools view -bS -> ${i}_cut.bam
done



for i in "liver1" "liver2" "liver3" "liver4"
do
samtools sort -o ${i}.sorted.bam ${i}_cut.bam; samtools index ${i}.sorted.bam
samtools view -h ${i}.sorted.bam | python /public/home/dk_dyf/songxinhui/biosoftware/ATAC-seq-master/removeChrom.py - - NC_006295.1 | samtools view -bh -> ${i}.noMT.bam
samtools sort -@ 40 -o ${i}.sorted.noMT.bam ${i}.noMT.bam; samtools index -@ 40 ${i}.sorted.noMT.bam
samtools view -@ 40 -bh -f 3 ${i}.sorted.noMT.bam > ${i}.filt.noMT.bam
samtools sort -@ 40 -o ${i}sfn.bam ${i}.filt.noMT.bam; samtools index -@ 40 ${i}sfn.bam
samtools flagstat -@ 40 ${i}sfn.bam > ${i}sfn.stat
done



cp *sfn.bam /public/home/dk_dyf/songxinhui/ATAC-seq/liver/05bedtools