Hello,

I am encountering an issue while using riboWaltz. I have an aligned, sorted BAM file generated using Bowtie with the Ensembl release 113 transcriptome reference FASTA file. For the riboWaltz annotation, I used the corresponding GTF file from the same Ensembl release. However, I am facing a mismatch between the transcript IDs in the BAM file and the annotation table.

Could you please guide me on how to correctly frame the annotation table to resolve this issue? Specifically:

Should the transcript IDs in the BAM file and the annotation table match exactly, including version numbers (e.g., ENST00000335137.1 vs. ENST00000335137)?

Are there any preprocessing steps required for the GTF or FASTA files before creating the annotation table with riboWaltz?

Thank you for your assistance!