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Gffreadのコマンド

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いつも忘れてしまうので、自分用にメモ
samtoolsをインストールし、PATHを通しておくと後々困らなくていいかも。

GTF → GFF3

gffread -E my.gtf -g my_genome.fasta -o- > my.gff3
#もしくは
gffread -E my.gtf -g my_genome.fasta -o my.gff3

※gene行の代わりにtranscripts行ができます。
※ゲノム配列のインデックスファイル(my_genome.fasta.fai)が必要ですが、samtoolsがインストールしてあれば勝手に作ってくれるので問題ないと思います

GFF3 → GTF

gffread -E my.gff3 -g my_genome.fasta -T -o- > my.gtf
#もしくは
gffread -E my.gff3 -g my_genome.fasta -T -o my.gtf

GFF3 → Exon・CDS・Protein sequences

gffread -E my.gff3 -g my_genome.fasta -w my_exons.fasta -x my_cds.fasta -y my_protein.fasta 

もっと詳しいオプションが見たい!という方は

gffread -h

で確認できます。

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