stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned/108TRA/108TRA.gtf -l 108TRA aligned/108TRA/108TRA.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned/112A/112A.gtf -l 112A aligned/112A/112A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned/113A/113A.gtf -l 113A aligned/113A/113A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned/114A/114A.gtf -l 114A aligned/114A/114A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned/122A/122A.gtf -l 122A aligned/122A/122A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned/124A/124A.gtf -l 124A aligned/124A/124A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned/126A/126A.gtf -l 126A aligned/126A/126A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned/127A/127A.gtf -l 127A aligned/127A/127A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned/130A/130A.gtf -l 130A aligned/130A/130A.sorted.bam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/17F24T/17F24T_1.fq.gz -2 CRC/16samples/17F24T/17F24T_2.fq.gz -S aligned-16/17F24T/17F24T.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/105TRA/105TRA_1.fq.gz -2 CRC/16samples/105TRA/105TRA_2.fq.gz -S aligned-16/105TRA/105TRA.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/109TRA/109TRA_1.fq.gz -2 CRC/16samples/109TRA/109TRA_2.fq.gz -S aligned-16/109TRA/109TRA.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/110A/110A_1.fq.gz -2 CRC/16samples/110A/110A_2.fq.gz -S aligned-16/110A/110A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/113A/113A_1.fq.gz -2 CRC/16samples/113A/113A_2.fq.gz -S aligned-16/113A/113A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/114A/114A_1.fq.gz -2 CRC/16samples/114A/114A_2.fq.gz -S aligned-16/114A/114A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/120A/120A_1.fq.gz -2 CRC/16samples/120A/120A_2.fq.gz -S aligned-16/120A/120A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/121A/121A_1.fq.gz -2 CRC/16samples/121A/121A_2.fq.gz -S aligned-16/121A/121A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/122A/122A_1.fq.gz -2 CRC/16samples/122A/122A_2.fq.gz -S aligned-16/122A/122A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/124A/124A_1.fq.gz -2 CRC/16samples/124A/124A_2.fq.gz -S aligned-16/124A/124A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/126A/126A_1.fq.gz -2 CRC/16samples/126A/126A_2.fq.gz -S aligned-16/126A/126A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/136A/136A_1.fq.gz -2 CRC/16samples/136A/136A_2.fq.gz -S aligned-16/136A/136A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/140A/140A_1.fq.gz -2 CRC/16samples/140A/140A_2.fq.gz -S aligned-16/140A/140A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/143A/143A_1.fq.gz -2 CRC/16samples/143A/143A_2.fq.gz -S aligned-16/143A/143A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/153A/153A_1.fq.gz -2 CRC/16samples/153A/153A_2.fq.gz -S aligned-16/153A/153A.sam
hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/154A/154A_1.fq.gz -2 CRC/16samples/154A/154A_2.fq.gz -S aligned-16/154A/154A.sam
samtools sort -@ 12 -o aligned-16/17F24T/17F24T.sorted.bam aligned-16/17F24T/17F24T.sam
samtools sort -@ 12 -o aligned-16/105TRA/105TRA.sorted.bam aligned-16/105TRA/105TRA.sam
samtools sort -@ 12 -o aligned-16/109TRA/109TRA.sorted.bam aligned-16/109TRA/109TRA.sam
samtools sort -@ 12 -o aligned-16/110A/110A.sorted.bam aligned-16/110A/110A.sam
samtools sort -@ 12 -o aligned-16/113A/113A.sorted.bam aligned-16/113A/113A.sam
samtools sort -@ 12 -o aligned-16/114A/114A.sorted.bam aligned-16/114A/114A.sam
samtools sort -@ 12 -o aligned-16/120A/120A.sorted.bam aligned-16/120A/120A.sam
samtools sort -@ 12 -o aligned-16/121A/121A.sorted.bam aligned-16/121A/121A.sam
samtools sort -@ 12 -o aligned-16/122A/122A.sorted.bam aligned-16/122A/122A.sam
samtools sort -@ 12 -o aligned-16/124A/124A.sorted.bam aligned-16/124A/124A.sam
samtools sort -@ 12 -o aligned-16/126A/126A.sorted.bam aligned-16/126A/126A.sam
samtools sort -@ 12 -o aligned-16/136A/136A.sorted.bam aligned-16/136A/136A.sam
samtools sort -@ 12 -o aligned-16/140A/140A.sorted.bam aligned-16/140A/140A.sam
samtools sort -@ 12 -o aligned-16/143A/143A.sorted.bam aligned-16/143A/143A.sam
samtools sort -@ 12 -o aligned-16/153A/153A.sorted.bam aligned-16/153A/153A.sam
samtools sort -@ 12 -o aligned-16/154A/154A.sorted.bam aligned-16/154A/154A.sam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/17F24T/17F24T.gtf -l 17F24T aligned-16/17F24T/17F24T.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/105TRA/105TRA.gtf -l 105TRA aligned-16/105TRA/105TRA.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/109TRA/109TRA.gtf -l 109TRA aligned-16/109TRA/109TRA.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/110A/110A.gtf -l 110A aligned-16/110A/110A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/113A/113A.gtf -l 113A aligned-16/113A/113A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/114A/114A.gtf -l 114A aligned-16/114A/114A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/120A/120A.gtf -l 120A aligned-16/120A/120A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/121A/121A.gtf -l 121A aligned-16/121A/121A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/122A/122A.gtf -l 122A aligned-16/122A/122A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/124A/124A.gtf -l 124A aligned-16/124A/124A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/126A/126A.gtf -l 126A aligned-16/126A/126A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/136A/136A.gtf -l 136A aligned-16/136A/136A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/140A/140A.gtf -l 140A aligned-16/140A/140A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/143A/143A.gtf -l 143A aligned-16/143A/143A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/153A/153A.gtf -l 153A aligned-16/153A/153A.sorted.bam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/154A/154A.gtf -l 154A aligned-16/154A/154A.sorted.bam
ls
samtools sort -@ 12 -o aligned-16/121A/121A.sorted.bam aligned-16/121A/121A.sam
stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned-16/121A/121A.gtf -l 121A aligned-16/121A/121A.sorted.bam
stringtie --merge -p 12 -G gencode.v31.annotation.gtf -o 16samples_merged.gtf mergelist-16samples.txt
ls