[miso-users] problem with GFF file

[Yarden Katz]

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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