[miso-users] problem with GFF file

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

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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