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The reference name would be like this.

>ENST00000290810 cdna chromosome:GRCh38:16:66802878:66830976:-1 gene:ENSG00000159593.15 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:NAE1 description:NEDD8 activating enzyme E1 subunit 1 [Source:HGNC Symbol;Acc:HGNC:621]

The old cold will store the transcript id as ENST00000290810 cdna chromosome:GRCh38:16:66802878:66830976:-1 gene:ENSG00000159593, which was not able to use in the converting transcriptome locations to genome locations.

The reference name would be like this. 
>`>ENST00000290810 cdna chromosome:GRCh38:16:66802878:66830976:-1 gene:ENSG00000159593.15 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:NAE1 description:NEDD8 activating enzyme E1 subunit 1 [Source:HGNC Symbol;Acc:HGNC:621]`

The old cold will store the transcript id as `ENST00000290810 cdna chromosome:GRCh38:16:66802878:66830976:-1 gene:ENSG00000159593`, which was not able to use in the converting transcriptome locations to genome locations.
@yuukiiwa yuukiiwa merged commit 6491ca7 into GoekeLab:dev Nov 24, 2023
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2 participants