Question: phytozome gtf file
0
gravatar for aj123
2.2 years ago by
aj12370
United States
aj12370 wrote:

Hi,

I have the phytozome Maize gff3 file but when I use gffread to convert to gtf something goes wrong with the created gtf and it doesnt work properly. is there some place i could get v3 genome fasta, gff3 and gtf from? preferably not from Gramene.

plant next-gen gff assembly genome • 1.0k views
ADD COMMENTlink modified 9 months ago by LP10 • written 2.2 years ago by aj12370

Have you managed to overcome the problem you had with the gtf file created from gff3? Did it finally run successfully? I have the same problem with my sorghum gff3 file.

ADD REPLYlink written 9 months ago by LP10

Could you provide a link to the gff3 file ? I can maybe help you.

ADD REPLYlink written 9 months ago by Juke-341.2k

I tried to provide the link, but I failed. The link requires one to have an existing account with phytozome. In other words if you have an account you will be required to login in order to access the gff file (Sbicolor_454_v3.1.1.gene.gff3) from your side. If your are not registered on Phytozome, unfortunately you can't access the link. Please help!

ADD REPLYlink written 8 months ago by LP10

You can download it and share it by dropbox

ADD REPLYlink written 8 months ago by Juke-341.2k

Could you provide a link to the gff3 file ? I can maybe help you.

ADD REPLYlink written 9 months ago by Juke-341.2k
1

If the file is only available to registered members then it may not be legal to share it directly with third-parties. You could register on phytozome site to access the file. Accounts appear to be free.

ADD REPLYlink written 8 months ago by genomax52k

Hi Juke-34,

It is very easy and free to register on phytozome - thanks to genomax for providing the link. By registering on phytozome, you will not only access sorghum genome, but also other genomes that may be of interest to you.

I really do need someone to show or instruct me how it is done to correctly covert gff file into gtf format. I will really appreciate it.

ADD REPLYlink written 8 months ago by LP10
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