*_genes.out duplicate genes

[ncbi]

*_genes.out duplicate genes

[dodoflyy]

Then how TPMCalculator identify gene copies? Here my GTF record only the first row's feature is "gene" others are "transcript"
And I can't see anything special of last 2 transcript from attributes.

$ grep "ENSG00000235538" gencode.v35.annotation.gtf | awk -v FS="\t" '$3!="exon" {print $9}'
gene_id "ENSG00000235538.3"; gene_type "lncRNA"; gene_name "AL078602.1"; level 2; tag "ncRNA_host"; havana_gene "OTTHUMG00000195978.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000665613.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-201"; level 2; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000518669.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000671100.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-202"; level 2; tag "basic"; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000522294.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000657614.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-203"; level 2; tag "basic"; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000507375.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000665405.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-204"; level 2; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000505809.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000669147.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-205"; level 2; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000506093.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000657157.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-206"; level 2; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000512883.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000667749.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-207"; level 2; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000506923.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000664207.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-208"; level 2; tag "basic"; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000509534.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000659903.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-209"; level 2; tag "basic"; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000508554.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000666400.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-210"; level 2; tag "basic"; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000521262.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000452944.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-211"; level 2; transcript_support_level "5"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000043020.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000669856.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-212"; level 2; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000512193.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000657138.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-213"; level 2; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000513259.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000659063.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-214"; level 2; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000527573.1";
gene_id "ENSG00000235538.3"; transcript_id "ENST00000654484.1"; gene_type "lncRNA"; gene_name "AL078602.1"; transcript_type "lncRNA"; transcript_name "AL078602.1-215"; level 2; tag "basic"; tag "TAGENE"; havana_gene "OTTHUMG00000195978.1"; havana_transcript "OTTHUMT00000527575.1";

[r78v10a07]

Hi,
This is the normal way TPMCalculator quantify RNA-Seq abundance on copies for a same gene. If you look at the output, the third column is the starting coordinate of the gene. In your example, each gene copy starts in a different position. TPMCalculator uses #1, #2, #3 ... to identify the copies.

[r78v10a07]

We identify the copies using the genomic coordinates. If the transcripts of a same gene are in different genomic region and they don't overlap we mark that as a copy of the same gene