第五步为optional
5| Examine how the transcripts compare with the reference annotation (optional):
$ gffcompare –r chrX_data/genes/chrX.gtf –G –o merged stringtie_merged.gtf
第六步：
6| Estimate transcript abundances and create table counts for Ballgown:
$ stringtie -e -B -p 8 -G stringtie_merged.gtf -o ballgown/ERR188044/ERR188044_chrX.gtf ERR188044_chrX.bam(之前samtools sort之后得到的bam文件)
合并的20samples：
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/17F24T/17F24T.gtf aligned/17F24T/17F24T.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/105TRA/105TRA.gtf aligned/105TRA/105TRA.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/108TRA/108TRA.gtf aligned/108TRA/108TRA.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/109TRA/109TRA.gtf aligned/109TRA/109TRA.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/110A/110A.gtf aligned/110A/110A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/112A/112A.gtf aligned/112A/112A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/113A/113A.gtf aligned/113A/113A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/114A/114A.gtf aligned/114A/114A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/120A/120A.gtf aligned/120A/120A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/121A/121A.gtf aligned/121A/121A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/122A/122A.gtf aligned/122A/122A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/124A/124A.gtf aligned/124A/124A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/126A/126A.gtf aligned/126A/126A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/127A/127A.gtf aligned/127A/127A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/130A/130A.gtf aligned/130A/130A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/136A/136A.gtf aligned/136A/136A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/140A/140A.gtf aligned/140A/140A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/143A/143A.gtf aligned/143A/143A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/153A/153A.gtf aligned/153A/153A.sorted.bam
stringtie -e -B -p 12 -G 20samples_merged.gtf -o ballgown-20samples/154A/154A.gtf aligned/154A/154A.sorted.bam
ls
创建ballgown-10samples文件夹，里面有各个样本各自的文件夹
利用组装好的非冗余的转录本文件即stringtie_merged.gtf 和samtools sort得到的bam文件，执行下面的脚本:
stringtie -e -B -p 12 -G 10samples_merged.gtf -o ballgown-10samples/105TRA/105TRA.gtf aligned/105TRA/105TRA.sorted.bam
stringtie -e -B -p 12 -G 10samples_merged.gtf -o ballgown-10samples/108TRA/108TRA.gtf aligned/108TRA/108TRA.sorted.bam
stringtie -e -B -p 12 -G 10samples_merged.gtf -o ballgown-10samples/112A/112A.gtf aligned/112A/112A.sorted.bam
stringtie -e -B -p 12 -G 10samples_merged.gtf -o ballgown-10samples/113A/113A.gtf aligned/113A/113A.sorted.bam
stringtie -e -B -p 12 -G 10samples_merged.gtf -o ballgown-10samples/114A/114A.gtf aligned/114A/114A.sorted.bam
stringtie -e -B -p 12 -G 10samples_merged.gtf -o ballgown-10samples/122A/122A.gtf aligned/122A/122A.sorted.bam
stringtie -e -B -p 12 -G 10samples_merged.gtf -o ballgown-10samples/124A/124A.gtf aligned/124A/124A.sorted.bam
stringtie -e -B -p 12 -G 10samples_merged.gtf -o ballgown-10samples/126A/126A.gtf aligned/126A/126A.sorted.bam
stringtie -e -B -p 12 -G 10samples_merged.gtf -o ballgown-10samples/127A/127A.gtf aligned/127A/127A.sorted.bam
stringtie -e -B -p 12 -G 10samples_merged.gtf -o ballgown-10samples/130A/130A.gtf aligned/130A/130A.sorted.bam
开始运行时报错，error：input file –e cannot be found!
搜索后发现从PDFcopy过来时，粘贴为以下内容：
stringtie –e –B -p 8 -G stringtie_merged.gtf -o ballgown/ERR188044/ERR188044_chrX.gtf ERR188044_chrX.bam
其中–e –B前面横线不应那么长，应该和-p一样，报错原因是 Stringtie error message ！！！！！
Has the above command line been copy / pasted from your scripts? Note that –e and –B (with dash) are different from -e and -B (with hyphen), and command line parameters are indicated by hyphens, not dashes.
就因为是粘贴过来的（尤其是PDF），所以格式啥的错了！！
最后每条命令生成1个.gtf文件，5个.ctab文件
创建ballgown-16samples文件夹，里面有各个样本各自的文件夹
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/17F24T/17F24T.gtf aligned-16/17F24T/17F24T.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/105TRA/105TRA.gtf aligned-16/105TRA/105TRA.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/109TRA/109TRA.gtf aligned-16/109TRA/109TRA.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/110A/110A.gtf aligned-16/110A/110A.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/113A/113A.gtf aligned-16/113A/113A.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/114A/114A.gtf aligned-16/114A/114A.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/120A/120A.gtf aligned-16/120A/120A.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/121A/121A.gtf aligned-16/121A/121A.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/122A/122A.gtf aligned-16/122A/122A.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/124A/124A.gtf aligned-16/124A/124A.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/126A/126A.gtf aligned-16/126A/126A.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/136A/136A.gtf aligned-16/136A/136A.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/140A/140A.gtf aligned-16/140A/140A.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/143A/143A.gtf aligned-16/143A/143A.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/153A/153A.gtf aligned-16/153A/153A.sorted.bam
stringtie -e -B -p 12 -G 16samples_merged.gtf -o ballgown-16samples/154A/154A.gtf aligned-16/154A/154A.sorted.bam
ls