gtf error

[zxc1359]

Hi Jonas A:
I have tried to construct and index spliced pangenome graph using the this gtf，but an error has occurred. I tried to solve the problem but the result was not satisfactory. So, can you give me some guidance and I would appreciate you！
I am looking forward for your reply.
Best

1       Liftoff gene    20590   30676   .       +       .       gene_id "ENSG00000272438"; gene_version "1"; gene_source "havana"; gene_biotype "lncRNA"; coverage "1.0"; sequence_ID "0.980"; extra_copy_number "0"; copy_num_ID "ENSG00000272438_0"; 
1       Liftoff transcript      20590   30676   .       +       .       gene_id "ENSG00000272438"; gene_version "1"; transcript_id "ENST00000607769"; transcript_version "1"; gene_source "havana"; gene_biotype "lncRNA"; transcript_source "havana"; transcript_biotype "lncRNA"; tag "basic"; transcript_support_level "4"; Parent "ENSG00000272438"; extra_copy_number "0"; 
1       Liftoff exon    20590   20713   .       +       .       gene_id "ENSG00000272438"; gene_version "1"; transcript_id "ENST00000607769"; transcript_version "1"; exon_number "1"; gene_source "havana"; gene_biotype "lncRNA"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00003700027"; exon_version "1"; tag "basic"; transcript_support_level "4"; Parent "ENST00000607769"; ID "exon_79172"; extra_copy_number "0"; 
1       Liftoff exon    30450   30676   .       +       .       gene_id "ENSG00000272438"; gene_version "1"; transcript_id "ENST00000607769"; transcript_version "1"; exon_number "2"; gene_source "havana"; gene_biotype "lncRNA"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00003696845"; exon_version "1"; tag "basic"; transcript_support_level "4"; Parent "ENST00000607769"; ID "exon_79173"; extra_copy_number "0"; 

[IndexRegistry]: Checking for phasing in VCF(s).
[IndexRegistry]: Chunking inputs for parallelism.
[IndexRegistry]: Chunking FASTA(s).
[IndexRegistry]: Chunking VCF(s).
[IndexRegistry]: Chunking GTF/GFF(s).
[IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input.
[transcriptome] ERROR: Exons are not in correct order according to attributes (line 5).

[jonassibbesen]

Hi, this error happens because the exons are not sorted in the correct order according to the exon_number attribute. Would it be possible to share more of the gtf file? You can use this email if you prefer not so share it here: [email protected]