GFF与GTF格式怎么转换

GFF与GTF格式怎么转换

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GFF主要是用来注释基因组，格式如下：

J15gleangene2530843025309140.+.ID=Gglean067903;status=novel;J15gleanmRNA25308430253091400.976879+.ID=Gglean067903-TA;Parent=Gglean067903;status=novel;J15gleanCDS2530843025308501.+0Parent=Gglean067903-TA;J15gleanCDS2530864625309140.+0Parent=Gglean067903-TA;J15gleangene126763129003.+.ID=Gglean075841;status=novel;J15gleanmRNA1267631290031+.ID=Gglean075841-TA;Parent=Gglean075841;status=novel;J15gleanCDS126763126973.+0Parent=Gglean075841-TA;J15gleanCDS127285127628.+2Parent=Gglean075841-TA;J15gleanCDS127719127854.+0Parent=Gglean075841-TA;J15gleanCDS128049128185.+2Parent=Gglean075841-TA;

而GTF主要是用来对基因进行注释，格式如下：

J01gleanCDS69767317.+0transcript_id"Gglean025939-TA";gene_id"Gglean025939";J01gleanCDS79128162.+0transcript_id"Gglean025939-TA";gene_id"Gglean025939";J01gleanCDS82458413.+1transcript_id"Gglean025939-TA";gene_id"Gglean025939";J01gleanCDS84798790.+0transcript_id"Gglean025939-TA";gene_id"Gglean025939";J01gleanCDS94449708.-2transcript_id"Gglean025954-TA";gene_id"Gglean025954";J01gleanCDS97789935.-0transcript_id"Gglean025954-TA";gene_id"Gglean025954";J01gleanCDS1001210216.-2transcript_id"Gglean025954-TA";gene_id"Gglean025954";J01gleanCDS1029910754.-2transcript_id"Gglean025954-TA";gene_id"Gglean025954";J01gleanCDS1083810926.-0transcript_id"Gglean025954-TA";gene_id"Gglean025954";J01gleanCDS1101511082.-1transcript_id"Gglean025954-TA";gene_id"Gglean025954";

转换：

Cufflinks里面的工具gffread可以直接实现GFF与GTF的互相转换。

#gff2gtfgffreadmy.gff3-T-omy.gtf#gtf2gffgffreadmerged.gtf-o->merged.gff3

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