Customized gtf file from Ensembl version 109 GRCz11 (danRer11)

The gtf from Ensembl version 109 GRCz11 (danRer11) was filtered to remove transcripts on alternative chromosomes, readthrough transcripts and all non-coding transcripts from a protein-coding gene. In addition, all genes with the same gene name which overlaps were merged under the same gene id to avoid ambiguous reads.
The procedure to generate the gtf is described in the bash file attached.