Blank output When converting GFF3 file to GTF using either gffread or AGAT

Blank output When converting GFF3 file to GTF using either gffread or AGAT

1

Hi,

I am trying to convert gff3 file (please see below) to GTF. I used two tools suggested here gffread and agat here.

#gff-version 3
    Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    1   1345    .   +   .   ID=gene_1;Name=Os01g0293800 gene;coverage=0.997;sequence_ID=0.982;extra_copy_number=0;copy_num_ID=gene_1_0
    Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    1623    3128    .   -   .   ID=gene_6;Name=Os01g0293900 gene;coverage=0.999;sequence_ID=0.968;extra_copy_number=0;copy_num_ID=gene_6_0
    Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    20379   21605   .   -   .   ID=gene_7;Name=Os01g0294500 gene;coverage=0.999;sequence_ID=0.995;extra_copy_number=0;copy_num_ID=gene_7_0
    Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    48673   50214   .   -   .   ID=gene_5;Name=Os01g0294700 gene;coverage=1.0;sequence_ID=0.995;extra_copy_number=0;copy_num_ID=gene_5_0
    Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    102125  104501  .   -   .   ID=gene_4;Name=Os01g0295600 gene;coverage=1.0;sequence_ID=0.992;extra_copy_number=0;copy_num_ID=gene_4_0
    Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    105502  108051  .   -   .   ID=gene_3;Name=Os01g0295700 gene;coverage=0.996;sequence_ID=0.991;extra_copy_number=0;copy_num_ID=gene_3_0
    Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    114102  118497  .   -   .   ID=gene_2;Name=Os01g0295900 gene;coverage=1.0;sequence_ID=0.997;extra_copy_number=0;copy_num_ID=gene_2_0
    Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    119424  122381  .   -   .   ID=gene_21;Name=Os01g0296000 gene;coverage=1.0;sequence_ID=0.995;extra_copy_number=0;copy_num_ID=gene_21_0
    Bg_94-1_CX35|chr01_10700000_16500000    Liftoff gene    122555  127107  .   +   .   ID=gene_14;Name=Os01g0296100 gene;coverage=0.996;sequence_ID=0.992;extra_copy_number=0;copy_num_ID=gene_14_0

I was using following commands;
AGAT-

agat_convert_sp_gff2gtf.pl --gff genes.gff -o genes.gtf

gffread-

gffread -E -F -O -T genes.gff -o genes.gtf

Both giving me an empty output (AGAT just retrive # comment).
Can someone help me in this regard?
Thank you!


agat


gffread


conversion

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