第四步：Merge transcripts from all samples:
warning: 此處的mergelist.txt是自己創(chuàng)建的，需要包含之前output.gtf文件的路徑
10samples和16samples中有重復的，所以去掉重復，合并到一個文件夾中，新文件夾有20個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
(用記事本創(chuàng)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盤AAA-LY文件夾中)
命令行：
(base) luoyang@DESKTOP-AO2ICCR:/mnt/d/AAA-臺式機-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：
用記事本創(chuàng)建了mergelist.txt文件，mergelist-16samples.txt保存在D盤AAA-LY文件夾中
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
