Hi @tgray4
By any chance, have you submitted StringTie using two options, prediction of gene models and read counting, in the same job? I believe StringTie does not support this anymore. A proper workflow is: create gene models for every sample, merge individual gene models into a single “master” annotation using StringTie merge, and use the master annotation for read counting. The reads can be counted with StringTie or any other software, for example, featureCounts. For read counting with StringTie disable gene prediction. Read counting should be done with the same annotation, for sake of comparison, hence, the two options were made incompatible.
If I misunderstood the issue, share the history, so people can check what is going on.
Kind regards,
Igor
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