Key ID for gene name was not found on GTF line

[ncbi]

Key ID for gene name was not found on GTF line

[r78v10a07]

Hi,
TPMCalculator cannot read GFF files. You need to convert the GFF to GTF.
Have a look at this threads on how to convert GFF to GTF.
https://www.biostars.org/p/45791/

[Liyong-Zhang]

Hello,

Sounds good. I will convert to GTF file first before running tpmcalculator. Thanks.

[sagarutturkar]

I have similar issue. I downloaded GFF file from here and then converted to GTF format using AGAT tool:

agat_convert_sp_gff2gtf.pl --gff C_auris_B11221_features.gff -o C_auris_B11221.gtf

A snapshot of GTF file is attached. I get an error as:

Reading GTF file ...
Key gene for gene name was not found on GTF line.
Error processing GTF line at Chromosome level:

PGLS01000002_C_auris_B11221     CGD     exon    1330    2913    .       +       .       ID "CJI97_001076-T-E1"; Parent "CJI97_001076-T"; gene_id CJI97_001076; transcript_id "CJI97_001076-T"

See attached: test.gtf.txt

Do you have any suggestions to make this work?

Thanks