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