Hi Andrey,

By default, the pipeline requires polyA tails for reporting novel unspliced isoforms. I’d like to ask whether it’s possible to report unspliced isoforms without polyA tails by adjusting the --polya_requirement parameter.

In current standardlized workflows, both the PacBio Iso-Seq and ONT Dorado pipelines typically trim polyA tails during preprocessing, which means no polyA tails are detected downstream. However, for certain transposable element–derived transcripts (e.g., L1-derived), although they are unspliced, they do possess polyA tails in their mature form.

Therefore, I have two related suggestions:

1. Add the --has_polya parameter.
   In addition to the default --polya_requirement “auto” setting, it would be helpful to add explicit options to indicate whether the input data are expected to contain polyA tails. An additional parameter (e.g., --has_polya or similar) could explicitly specify whether reads are expected to have polyA tails.
2. Extend the --polya_requirement parameter.
   This would allow users to report all mono-exonic isoforms regardless of detected polyA, with an appropriate caution note (e.g., “use at your own risk”). for certain transposable element–derived transcripts (e.g., L1-derived), although they are unspliced, they do expressed and very important. This option may bring false positive, but if my long-read data have polyA tails but have been trimmed during preprocessing, I can still choose to report unspliced mono-exonic isoforms, because I know my data is reliable.

That's all from my perspecttive and I'm looking foward to know more about your ideas.

Best,
Puwen