使用 gff2bed 将 gff文件转换为bed格式

 

001、gff3文件转bed

[root@pc1 test2]# ls
Capra_hircus.ARS1.108.gff3
[root@pc1 test2]# gff2bed <Capra_hircus.ARS1.108.gff3 > test.bed
Warning: If your Wiggle data is a significant portion of available system memory, use the --max-mem and --sort-tmpdir options, or use --do-not-sort to disable post-conversion sorting. See --help for more information.
[root@pc1 test2]# ls
Capra_hircus.ARS1.108.gff3  test.bed
[root@pc1 test2]# ll -h
total 343M
-rw-r--r--. 1 root root 171M Aug 10 18:45 Capra_hircus.ARS1.108.gff3
-rw-r--r--. 1 root root 173M Nov  9 15:02 test.bed

 

 

002、gff文件转bed

[root@pc1 test2]# ls
GCF_001704415.2_ARS1.2_genomic.gff
[root@pc1 test2]# gff2bed <GCF_001704415.2_ARS1.2_genomic.gff > test.bed
Warning: If your Wiggle data is a significant portion of available system memory, use the --max-mem and --sort-tmpdir options, or use --do-not-sort to disable post-conversion sorting. See --help for more information.
[root@pc1 test2]# ls
GCF_001704415.2_ARS1.2_genomic.gff  test.bed
[root@pc1 test2]# ll -h
total 633M
-rw-r--r--. 1 root root 317M Jul 16 06:54 GCF_001704415.2_ARS1.2_genomic.gff
-rw-r--r--. 1 root root 316M Nov  9 15:07 test.bed

 

参考：https://www.jianshu.com/p/d3d1fd52c2f1