Question: IGB won't open .gff file.
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gravatar for sj93
4 weeks ago by
sj9310
sj9310 wrote:

The IGB website says their program supports many different file formats, including gff. I have saved a genome from NCBI in several different file formats to my computer (using Ubuntu), but when I go to open the custom genome from IGB, it only recognizes the .fna file type, when I have genomes saved as .gbff and .gff in the same folder. It's like the program won't recognize these file types saved on my computer. Does anyone know why this might be happening? Thanks in advance.

sequencing igb gff gff3 genome • 154 views
ADD COMMENTlink written 4 weeks ago by sj9310

Could you provide a sample of your gff fille ? Do you load the fasta separately or is it embedded in your gff ?

ADD REPLYlink written 4 weeks ago by Juke-342.0k

The fasta is not embedded, I tried it separately for comparison. I'm not sure what the best way to provide a link to my gff file would be, but the file is available on the top of the page at this location https://www.ncbi.nlm.nih.gov/genome/24088.

ADD REPLYlink written 4 weeks ago by sj9310
1

The GFF contains the annotation. It can sometimes contain the "genome sequence" using embedded FASTA that Juke-34 refers to, but more often the genome sequence is in a FASTA file (extension .fa, .fasta, or .fna sometimes from NCBI). You can download the FASTA from NCBI too and probably will open that first and then the annotation as GFF

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by cmdcolin1.1k

Thank you very much! :)

ADD REPLYlink written 4 weeks ago by sj9310

This gff file is completely stupid, never seen that before. It doesn't contain anything interesting, no structural annotation (position of feature like gene, trna, pseudogene, etc). It looks like description of sequences of an assembly. It describes the size of 80 000 sequences. So it's a gff of an assembly... I'm wondering how useful that could be ???

So according to this gff file there is nothing to display, so it's normal you don't see anything in IGB.

ADD REPLYlink written 4 weeks ago by Juke-342.0k

This is a mitochondrial genome (not a full genome) AFAI see.

ADD REPLYlink written 4 weeks ago by genomax64k

She/he said at the top of the page...

Anguilla rostrata (American eel) Representative genome: Anguilla rostrata (assembly ASM160608v1) Download sequences in FASTA format for genome Download genome annotation in GFF, GenBank format BLAST against Anguilla rostrata genome

I don’t think she/he talks about the mitochondrial genome.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Juke-342.0k
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