Some transcripts are missing agat_convert_sp_gxf2gxf.pl

[IrinaVKuznetsova]

Describe the bug Not sure if it is a standard behaviour, but I am trying to add missing information (e.g transcript, exon or gene) to my GTF file. Using: agat_convert_sp_gxf2gxf.pl --gtf $INGTF --out $GFFOUT to add missing transcripts to GTF file, but for some features they are missing. Using agat_convert_sp_gff2gtf.pl --gff $GFFOUT --out $OUTGTF --keep_header=true to convert to GTF format.

General (please complete the following information):

• AGAT version (Version: v1.4.0]
• AGAT installation/use [Conda, conda install -c bioconda agat]
• OS: Ubuntu

To Reproduce downloaded GTF from ensembl

Expected behavior expect that the row with missing transcripts info is added to TGF 1H IPK gene 92282224 92282629 xxx 1H IPK transcript 92282224 92282629 xxx 1H IPK exon 92282224 92282629 xxx

[Juke34]

Can you share a sample with what you provide in and pointing what is missing in the output?