第三步-StringTie-assemble-得到.gtf文件

Assemble and quantify expressed genes and transcripts

第三步：Assemble transcripts for each sample:

(base) luoyang@DESKTOP-AO2ICCR:/mnt/d/AAA-台式机-LY-WorkSpace$ stringtie -p 12 -G gencode.v31.annotation.gtf -o aligned/105TRA/105TRA.gtf -l 105TRA aligned/105TRA/105TRA.sorted.bam

最后生成105TRA.gtf文件

10samples:

stringtie -p 12 -G gencode.v31.annotation.gtf -o  aligned/105TRA/105TRA.gtf -l 105TRA aligned/105TRA/105TRA.sorted.bam

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

---

16samples:

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