Problem loading Gff file

[Hazel Perry]

Hi,
I have downloaded a GFF file from genbank and am trying to open it with my genome in IGV.  The program recognises it, by asking me if I want a index file to be created, but when I say yes it wont load.  The progress bar in the bottom right seems to be doing something but it just keeps going back to 0 when it says it's almost loaded (eg it goes from 1110M of 1,115M to 105M of 1,115M, then does the same again).  It's been doing this for about an hour now but nothing has loaded, is this a bug or something with the file (it has come straight from genbank, all I have done is unzip it).
Thanks
Hazel

[Jim Robinson]

How large is the file?

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[Hazel Perry]

212MB

[Jim Robinson]

Send me a link to the file and I will investigate. 

Jim

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[Hazel Perry]

ftp://ftp.ncbi.nlm.nih.gov/genomes/Poecilia_reticulata/Gnomon/

I have downloaded and am trying to open the scaffolds file.

Thanks
Hazel

[Jim Robinson]

The organization of that species directory is a bit of a mess,  how did you define the reference assembly for this gff file?

Jim

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[Jim Robinson]

I tried indexing the file with igvtools and it failed, telling me the file is not sorted by genomic start position.    After sorting the index succeeded.   I suggest you first sort then index the file,  rather than let it try automatically.   To do this select "Tools > Run igvtools..."   and do as the screenshots below indicate.  After indexing load the sorted gff3 file.

The other problem you might encounter is a mismatch in reference sequence (scaffold) names between the reference fasta and the gff.   This often occurs with NCBI hosted files,  so if after getting past the indexing step you see nothing check that.

 

[Hazel Perry]

It would appear that both of those are an issue.  I've indexed the file and it is loading (very slowly) but having looked the scaffold names are not the same as in my reference file so I'll have to re-do them as well.

Thanks for your help.
I'll come back if re-naming doesn't work.
Hazel

[Sara López]

Hi!

I have the same problem than Hazel. I have a genome (982 MB) and an annotation file (93MB). It was said that the annotation file was not sorted, so I did it, and later on I indexed it. It also seems that the name for chromosomes were not the same on the genome and the annotation file, so I created a tab file as indicated in the manual. Doing all that, re-starting again the software and so on, I get the same, as if something is loading but when it is close to the end, it starts again.
When loading the genome, I can see the chromosomes, but the nucleotide sequences is not display. In the annotation track, I can see that it appears the name on the right, but nothing else. The software is working well for other genomes such as human or tomato 2.40.
I am using windows 7, and the software version is IGV 2.3.57 (74)

Thanks

Sara

[Jim Robinson]

Hi,

Are you using a ".genome" file with the annotation file included?   If you are using an indexed annotation file do not include it in the  ".genome file",  rather leave it out (just specify fasta and alias file) and load it directly from the file menu.   If you've tried that let me know and we'll dig further.

Jim

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[Sara López]

Hi Jim, thanks for your message. I was using a genome without any gene annotation. I was loading the genome from the genome tab, including the alias in the same folder, and then loading a file with the annotations. I think that the genome is ok (now I can see the nucleotide sequence) but although the track of the annotation appers, there is no information about the genes and it seems that it is uploading information endless.

Thanks

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[Jim Robinson]

Are these files publicly available (fasta and gff),  can you send me a link to them?

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[Sara López]

Sure!

ftp://ftp.solgenomics.net/genomes/Solanum_pennellii/

I was using Spenn.fasta as genome and spenn_v2.0_gene_models_annot.gff as annotations (previously sorted using the igv tools)

Thanks

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[Jim Robinson]

OK,  I see if I can add this to our hosted list, but it might be the end of the week or weekend before I get to it.

Jim

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[Sara López]

Thanks Jim! I really appreciate it. Any help will be wellcome

Sara

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[Sara López]

Hi!

At the end we changed the name of the chromosomes in the genome file according tot he name of chromosomes in the gff file and it works! Maybe the problem was in the tab file

Thank you for your help

Sara

[Chooseel Bunsuwansakul]

it works.

Thanks for the solution.

18/10/2022

chooseel