[miso-users] problem with GFF file

[Akula, Nirmala (NIH/NIMH) [C]]

Hi,

The GFF file has only "transcript and "exon" entries. No "genes".

Thanks,
Nirmala

-----Original Message-----
From: Yarden Katz [mailto:yarden.katz at gmail.com] On Behalf Of Yarden Katz
Sent: Friday, July 17, 2015 5:55 PM
To: Akula, Nirmala (NIH/NIMH) [C]
Cc: miso-users at mit.edu
Subject: Re: [miso-users] problem with GFF file

Hi,

Does your GFF file contain "gene" entries, or just "transcript" and "exon" entries?

The "gene" entries are used to determine genes.  

Yarden

On Jul 17, 2015, at 5:16 PM, Akula, Nirmala (NIH/NIMH) [C] <akulan at mail.nih.gov> wrote:

> Hi,
>  
> I converted GTF file (generated by Cufflinks) to GFF3 format using Cufflinks using the following command:
>  
> gffread -E merged.gtf -o- >merged_gtfToGff3.gff3
>  
> When I try to index merged_gtfToGff3.gff3 file using MISO I see that 0 genes were loaded and genes.gff file is 0.
>  
> [akulan at helix stringtieGtfs_v1-0-3_cuffmerged]$ index_gff --index merged_gtfToGff3.gff3 mergedIndexedGff/
> Indexing GFF...
>   - GFF: /akulan/merged_gtfToGff3.gff3
>   - Outputting to: / akulan/mergedIndexedGff
> Loaded 0 genes
>   - Loading of genes from GFF took 199.95 seconds
> Outputting gene records in GFF format...
>   - Output file: /gpfs/gsfs4/users/akulan/transcriptome/stringtie/stringtieGtfs_v1-0-3_cuffmerged/mergedIndexedGff/genes.gff
>   - Serialization of genes from GFF took 13.24 seconds
> Indexing of GFF took 213.18 seconds.
>  
> Here are the top 5 lines from the gff3 file
> # gffread -E merged.gtf -o-
> ##gff-version 3
> chr1    Cufflinks       transcript      11869   14409   .       +       .       ID=TCONS_00000001;geneID=XLOC_000001;gene_name=DDX11L1
> chr1    Cufflinks       exon    11869   12227   .       +       .       Parent=TCONS_00000001
> chr1    Cufflinks       exon    12613   12721   .       +       .       Parent=TCONS_00000001
> chr1    Cufflinks       exon    13221   14409   .       +       .       Parent=TCONS_00000001
> chr1    Cufflinks       transcript      11869   29022   .       +       .       ID=TCONS_00000002;geneID=XLOC_000001;gene_name=DDX11L1
>  
> Any suggestions as to why the genes are not loaded from the gff file would be really helpful.
>  
> Thank you very much.
>  
> Regards,
> Nirmala
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