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：

J15     glean   gene    25308430        25309140        .       +       .       ID=Gglean067903; status=novel;J15     glean   mRNA    25308430        25309140        0.976879        +       .       ID=Gglean067903-TA; Parent=Gglean067903; status=novel;J15     glean   CDS     25308430        25308501        .       +       0       Parent=Gglean067903-TA;J15     glean   CDS     25308646        25309140        .       +       0       Parent=Gglean067903-TA;J15     glean   gene    126763  129003  .       +       .       ID=Gglean075841; status=novel;J15     glean   mRNA    126763  129003  1       +       .       ID=Gglean075841-TA; Parent=Gglean075841; status=novel;J15     glean   CDS     126763  126973  .       +       0       Parent=Gglean075841-TA;J15     glean   CDS     127285  127628  .       +       2       Parent=Gglean075841-TA;J15     glean   CDS     127719  127854  .       +       0       Parent=Gglean075841-TA;J15     glean   CDS     128049  128185  .       +       2       Parent=Gglean075841-TA;

而GTF主要是用来对基因进行注释，格式如下：

J01     glean   CDS     6976    7317    .       +       0       transcript_id "Gglean025939-TA"; gene_id "Gglean025939";J01     glean   CDS     7912    8162    .       +       0       transcript_id "Gglean025939-TA"; gene_id "Gglean025939";J01     glean   CDS     8245    8413    .       +       1       transcript_id "Gglean025939-TA"; gene_id "Gglean025939";J01     glean   CDS     8479    8790    .       +       0       transcript_id "Gglean025939-TA"; gene_id "Gglean025939";J01     glean   CDS     9444    9708    .       -       2       transcript_id "Gglean025954-TA"; gene_id "Gglean025954";J01     glean   CDS     9778    9935    .       -       0       transcript_id "Gglean025954-TA"; gene_id "Gglean025954";J01     glean   CDS     10012   10216   .       -       2       transcript_id "Gglean025954-TA"; gene_id "Gglean025954";J01     glean   CDS     10299   10754   .       -       2       transcript_id "Gglean025954-TA"; gene_id "Gglean025954";J01     glean   CDS     10838   10926   .       -       0       transcript_id "Gglean025954-TA"; gene_id "Gglean025954";J01     glean   CDS     11015   11082   .       -       1       transcript_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。

#gff2gtfgffread my.gff3 -T -o my.gtf#gtf2gffgffread merged.gtf -o- > merged.gff3

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