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@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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