How To Get Bed File For Genome?

Question

[GouthamAtla]

I have a Chip-Seq data. I ran Bowtie and MACS on that data. I got peak files like name.bed and name.xls. Now to annotate that peaks , I am using PeakAnnotator software where it requires the Annotation file which is a BED that to be obtained from Genome Table Browser. But I could not found there. Is there any way to Get BED file for Glycine_max genome?

Answer 1

[Vikas Bansal]

I just searched for G.max genome and found this database and they have genome files here. I downloaded "Gmax109gene.gff3" file and it looks like -

##gff-version 3
Gm01    phytozome6  gene    51481   61502   .   -   .   ID=Glyma01g00270;Name=Glyma01g00270
Gm01    phytozome6  mRNA    51481   61502   .   -   .   ID=PAC:16242891;Name=Glyma01g00270.1;PACid=16242891;Parent=Glyma01g00270
Gm01    phytozome6  CDS 61437   61502   .   -   0   Parent=PAC:16242891;PACid=16242891
Gm01    phytozome6  CDS 61167   61305   .   -   0   Parent=PAC:16242891;PACid=16242891
Gm01    phytozome6  CDS 60722   60780   .   -   2   Parent=PAC:16242891;PACid=16242891
Gm01    phytozome6  CDS 60339   60533   .   -   0   Parent=PAC:16242891;PACid=16242891
Gm01    phytozome6  CDS 59699   59814   .   -   0   Parent=PAC:16242891;PACid=16242891
Gm01    phytozome6  CDS 59420   59547   .   -   1   Parent=PAC:16242891;PACid=16242891
Gm01    phytozome6  CDS 59176   59284   .   -   2   Parent=PAC:16242891;PACid=16242891

There is a Readme file here where you can find more information about these files.

EDIT: And you can convert this gff file into BED (or any other format), basically just rearrange the columns.

Answer 2

[Alex Reynolds]

A gff2bed conversion script, part of the BEDOPS suite, is available here. This converts 1-based GFF3 files to 0-based, extended BED, following the UCSC specification.