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