RNA-SeQC: Failed to parse the GTF: Detected non-unique Exon ID

Question

[akulan]

Hi,

I am trying to run RNA-SeQC and got the following error: Failed to parse the GTF: Detected non-unique Exon ID: ENSE00001957285

I am using Homo_sapiens.GRCh38.87.gtf. It's an exon that is assigned to 3 different transcripts in the GTF. Did anyone encounter this problem? If so, is it better to remove the exons completely or change the names of such exons?

Thanks in advance for your responses.

Regards, Nirmala

[383882951]

I'm having the same problem now, have you solved it now? If you have solved this problem, could you tell me how did you solved it?

Answer 1

[Juke34]

You can de-factorize the exons running AGAT. You will get a dedicated exon for each transcript with a unique ID.

agat_convert_sp_gxf2gxf.pl --gff Homo_sapiens.GRCh38.87.gtf -o Homo_sapiens.GRCh38.87_agat.gtf

I do not know if the identifier has to be stored wihtin the exon_id attribute or not for RNA-SeQC, so if necessary you can copy the ID attribute and owerwrite the exon_id attribute with it using:

 agat_sp_manage_attributes.pl -gff file.gff  -att ID/exon_id -p exon --cp --overwrite -o output.gff

Then to have a proper GTF if you need to use GTF format you can run the command below.
NOTE: Since AGAT v1.0.0 you can expose the AGAT config file and set the default ouput to GTF. In such case the previous command will directly output GTF format.

agat_convert_sp_gff2gtf.pl --gff file.gff -o output.gtf

[GenoMax]

Juke34 can you show an example of how to do that? As the developer you may have that clear in your mind.