Two Isoforms with 4bp Difference

[x1han]

Dear Ying,

Thank you for developing Bambu – it is an amazing tool that has greatly assisted my research. I encountered an issue and would appreciate your insights:

After comparing the expression of newly identified isoforms, we observed two transcript isoforms from the same gene showing completely opposite expression trends (one upregulated, the other downregulated). These isoforms differ by only 4bp in one exon out of 11 exons.

My questions are:

1. Do you believe these two isoforms are likely to be real, or how would you assess their credibility? Given their minimal 4bp difference, they might be challenging to distinguish in downstream analyses (e.g., cross-dataset comparisons or protein prediction).
2. Since I am currently using default parameters, would you recommend filtering (e.g., adjusting NDR thresholds)? However, their opposing trends complicate this – retaining only one or merging them feels inappropriate. How would you suggest handling such cases?

Your guidance would be invaluable. Thank you for your time!

Best regards,
Xi