hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/105TRA/105TRA_1.fq.gz -2 CRC/10samples/105TRA/105TRA_2.fq.gz -S aligned/105TRA/105TRA.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/108TRA/108TRA_1.fq.gz -2 CRC/10samples/108TRA/108TRA_2.fq.gz -S aligned/108TRA/108TRA.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/112A/112A_1.fq.gz -2 CRC/10samples/112A/112A_2.fq.gz -S aligned/112A/112A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/113A/113A_1.fq.gz -2 CRC/10samples/113A/113A_2.fq.gz -S aligned/113A/113A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/114A/114A_1.fq.gz -2 CRC/10samples/114A/114A_2.fq.gz -S aligned/114A/114A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/122A/122A_1.fq.gz -2 CRC/10samples/122A/122A_2.fq.gz -S aligned/122A/122A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/124A/124A_1.fq.gz -2 CRC/10samples/124A/124A_2.fq.gz -S aligned/124A/124A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/126A/126A_1.fq.gz -2 CRC/10samples/126A/126A_2.fq.gz -S aligned/126A/126A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/127A/127A_1.fq.gz -2 CRC/10samples/127A/127A_2.fq.gz -S aligned/127A/127A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/130A/130A_1.fq.gz -2 CRC/10samples/130A/130A_2.fq.gz -S aligned/130A/130A.sam
samtools sort -@ 12 -o aligned/105TRA/105TRA.sorted.bam aligned/105TRA/105TRA.sam
samtools sort -@ 12 -o aligned/108TRA/108TRA.sorted.bam aligned/108TRA/108TRA.sam
samtools sort -@ 12 -o aligned/112A/112A.sorted.bam aligned/112A/112A.sam
samtools sort -@ 12 -o aligned/113A/113A.sorted.bam aligned/113A/113A.sam
samtools sort -@ 12 -o aligned/114A/114A.sorted.bam aligned/114A/114A.sam
samtools sort -@ 12 -o aligned/122A/122A.sorted.bam aligned/122A/122A.sam
samtools sort -@ 12 -o aligned/124A/124A.sorted.bam aligned/124A/124A.sam
samtools sort -@ 12 -o aligned/126A/126A.sorted.bam aligned/126A/126A.sam
samtools sort -@ 12 -o aligned/127A/127A.sorted.bam aligned/127A/127A.sam
samtools sort -@ 12 -o aligned/130A/130A.sorted.bam aligned/130A/130A.sam
ls