第四步-stringtie-merge-得到一个merged.gtf文件

第四步：Merge transcripts from all samples:

warning: 此处的mergelist.txt是自己创建的，需要包含之前output.gtf文件的路径

10samples和16samples中有重复的，所以去掉重复，合并到一个文件夹中，新文件夹有20个samples

stringtie --merge -p 12 -G gencode.v31.annotation.gtf -o 20samples_merged.gtf mergelist-20samples.txt

---

$ stringtie --merge -p 8 -G chrX_data/genes/chrX.gtf -o stringtie_merged.gtf chrX_data/mergelist.txt

10samples：

stringtie --merge -p 12 -G gencode.v31.annotation.gtf -o 10samples_merged.gtf mergelist-10samples.txt

(用记事本创建了mergelist.txt文件，

aligned/105TRA/105TRA.gtf

aligned/108TRA/108TRA.gtf

aligned/112A/112A.gtf

aligned/113A/113A.gtf

aligned/114A/114A.gtf

aligned/122A/122A.gtf

aligned/124A/124A.gtf

aligned/126A/126A.gtf

aligned/127A/127A.gtf

aligned/130A/130A.gtf

mergelist-10samples.txt保存在D盘AAA-LY文件夹中)

命令行：

(base) luoyang@DESKTOP-AO2ICCR:/mnt/d/AAA-台式机-LY-WorkSpace$ stringtie --merge -p 12 -G gencode.v31.annotation.gtf -o 10samples_merged.gtf mergelist-10samples.txt

得到10samples_merged.gtf文件

---

16samples：

用记事本创建了mergelist.txt文件，mergelist-16samples.txt保存在D盘AAA-LY文件夹中

aligned-16/17F24T/17F24T.gtf

aligned-16/105TRA/105TRA.gtf

aligned-16/109TRA/109TRA.gtf

aligned-16/110A/110A.gtf

aligned-16/113A/113A.gtf

aligned-16/114A/114A.gtf

aligned-16/120A/120A.gtf

aligned-16/121A/121A.gtf

aligned-16/122A/122A.gtf

aligned-16/124A/124A.gtf

aligned-16/126A/126A.gtf

aligned-16/136A/136A.gtf

aligned-16/140A/140A.gtf

aligned-16/143A/143A.gtf

aligned-16/153A/153A.gtf

aligned-16/154A/154A.gtf

stringtie --merge -p 12 -G gencode.v31.annotation.gtf -o 16samples_merged.gtf mergelist-16samples.txt