Question: How To Get Bed File For Genome?
0
gravatar for geek_y
7.3 years ago by
geek_y9.8k
Barcelona
geek_y9.8k wrote:

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?

bed chip-seq • 2.4k views
ADD COMMENTlink modified 7.3 years ago by Alex Reynolds28k • written 7.3 years ago by geek_y9.8k
3
gravatar for Vikas Bansal
7.3 years ago by
Vikas Bansal2.3k
Berlin, Germany
Vikas Bansal2.3k wrote:

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.

ADD COMMENTlink modified 7.3 years ago • written 7.3 years ago by Vikas Bansal2.3k
0
gravatar for Alex Reynolds
7.2 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

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.

ADD COMMENTlink written 7.2 years ago by Alex Reynolds28k
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