Question: Annotation In Gff3
0
gravatar for Daniel Fernández
6.7 years ago by
Lima, Perú
Daniel Fernández40 wrote:

Hi,

Can anybody tell me a program to find genes by homology that generate GFF3?

I tired AAT but only show me a table

I tried Exonerate but it give me a GFF2 and it can't load in artemis

If anybody tell me MAKER, yes it is very very useful, I tried to install it but it's very complicate for me, I tried to install it for 2 months and nothing.

And I read that is not recommended convert GFF2 to GFF3.

Can anybody help me, please?

Thanks

DNL

gff3 annotation gff • 2.4k views
ADD COMMENTlink modified 6.7 years ago by Christian2.7k • written 6.7 years ago by Daniel Fernández40
1

People in the Maker community are friendly. You should ask for help. Where are you stuck? My lab developed Maker. Maybe I could help you get it up and running.

ADD REPLYlink written 6.7 years ago by Zev.Kronenberg11k

Well, 5months ago I tried to install it. I remember that I can't install the RMBlast, I copy the executables in my $PATH, I run it and ok, but the maker did not recognize it, and I am confused because RMBlast have several binaries with the same name that Blast, so in my path I had binaries with the same name (no in same directory), and this is only one because some programs I can't install by the ./Build install, and when I installed these programs manually the maker did not recognize.

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by Daniel Fernández40

I trying to install MAKER again, in RepeatMasker wich RepBase is the one I have to download?RepBase17.05.embl.tar.gz or RepBase17.05.fasta.tar.gz.

ADD REPLYlink written 6.7 years ago by Daniel Fernández40

Let me check with my lab-mate tomorrow morning and get back to you. I am on Mountain time.

ADD REPLYlink written 6.7 years ago by Zev.Kronenberg11k

I think it is the EMBL file. I checked in my local install of maker and that's what I found in the RepeatMasker/Libraries directory.

ADD REPLYlink written 6.7 years ago by Zev.Kronenberg11k

Well it is the libraries not the RepBase, http://www.girinst.org/server/RepBase/index.php, I downloaded both RepBase17.05.###.tar.gz, but I don't know how install it, it doesn't have a readme or install file.

ADD REPLYlink written 6.7 years ago by Daniel Fernández40
1
gravatar for Christian
6.7 years ago by
Christian2.7k
Cambridge, US
Christian2.7k wrote:

genBlastG can produce GFF3 output.

genBlastG: using BLAST searches to build homologous gene models.

Bioinformatics (2011) 27 (15): 2141-2143.

ADD COMMENTlink written 6.7 years ago by Christian2.7k
0
gravatar for Ryan Thompson
6.7 years ago by
Ryan Thompson3.4k
TSRI, La Jolla, CA
Ryan Thompson3.4k wrote:

The Cufflinks suite includes a program called "gffread" that can convert GFF2 (also know as GTF) to GFF3 and vice versa. As long as your GFF2 file is well-formed, it should convert OK to GFF3. It should be worth a try.

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Ryan Thompson3.4k

I search in Cufflinks but I did not find the "gfftool", can you send me the link, please?

ADD REPLYlink written 6.7 years ago by Daniel Fernández40

Oops, it is actually called "gffread". I have edited my answer.

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by Ryan Thompson3.4k

I run the "gffread" but it show me an error: No such file or directory at ./gffread.pl line 27.

The line 27 is: open CONFIG, "/usr/users/ga002/corpasm/workarea/ricinus/conf/gffread.conf" or die $!;

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by Daniel Fernández40

Are you using an old version of Cufflinks? In the current version, gffread is a compiled executable, not a Perl script.

ADD REPLYlink written 6.7 years ago by Ryan Thompson3.4k

Sorry but what parameter I have to use to convert gff3 to gff2? I tried but without success

ADD REPLYlink written 6.7 years ago by Daniel Fernández40

Do you want to convert GFF2 to GFF3 or the reverse? The default is to output GFF3, and the -T option makes it output GFF2. Please read the help test for more information.

ADD REPLYlink written 6.7 years ago by Ryan Thompson3.4k

Sorry, GFF2 to GFF3, I tried with

gffread -E exonerate.gff2 -o out.gff3

but it doesn't work, the outgff3 size is 0 , I tried tha same but with the augustus.gff3, and work, what's the problem?

ADD REPLYlink written 6.7 years ago by Daniel Fernández40

That looks like the right usage. I'm not sure what the problem is. Check for any error messages produced.

ADD REPLYlink written 6.7 years ago by Ryan Thompson3.4k

No error message was produced, nothing, it's very rare. Before you test the gffread with exonerate.

ADD REPLYlink written 6.7 years ago by Daniel Fernández40
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