Gff3_to_gtf && gff3_to_bed

1.gff3_to_bed

Approadch 1:

利用TransDecoder的gff3_file_to_bed.pl脚本完成（conda 安装TransDecoder）

gff3_file_to_bed.pl /public/home/qtxu/rice_anotation/Rice_annotation/Tige7.0.gff3 >Tigr_MSU_7_raw.bed

#format the bed files!

sed 's/;LOC\S*\t/\t/g' Tigr_MSU_7_raw.bed |sed 's/ID=//g' >Tigr_MSU_7.bed

Approadch 2:

下载 Gff3ToBed（https://github.com/YoannPa/Gff3ToBed）

sudo chmod +x Gff3ToBed

# Example: Extract all data to a Bed file
./Gff3ToBed.sh gencode.v26.annotation.gff3 gff3 all both
# 

Approadch 3:

#下载# [BEDOPS v2.4.40](https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gff2bed.html#downloads)

#We can convert it to sorted BED data in the following manner:

$ gff2bed < foo.gff3
chr1    1049    1500    exon00002       .       -       USA     exon    0       ID=exon00002;Ontology_term="GO:0046703";Ontology_term="GO:0046704"
chr1    1299    1300    exon00001       .       +       Canada  exon    .       ID=exon00001;score=1;zeroLengthInsertion=True
chr1    2999    3902    exon00003       .       ?       Canada  exon    2       ID=exon00003;score=4;Name=foo
chr1    4999    5500    exon00004       .       .       .       exon    .       ID=exon00004;Gap=M8 D3 M6 I1 M6
chr1    6999    9000    exon00005       10      +       .       exon    1       ID=exon00005;Dbxref="NCBI_gi:10727410"

2.gff3_to_GTF

gff 2 gtf

gffread  gencode.v19.annotation.gff3  -T  -o   gencode.v19.gtf