Error, the references in bam are different from transcriptome annotation

[KONeill872]

Hi,

I got the following error when running my script:

Error, the references in bam are different from transcriptome annotation

It seems to throw this as my reads were aligned to the transcriptome and have the transcript version ID instead of just the transcript ID. Is it possible for the output of the prepare_transcript function to include the version number?

Thanks