Mihaela Pertea

There is no option in StringTie to output those extra potential "transcripts". Those 16 potential transcripts are just paths in the splicing graph that StringTie considers. In this case, once...

The -m parameter only controls the length of novel assembled transcripts. If you used the -G parameter, all the transcripts in the reference annotation will be considered as well, no...

This happens when your annotation file contains genes with non-overlapping transcripts. We consider this to be an annotation error. In this case we suggest to complete your downstream analysis by...

These parameters only apply to the novel transcripts assembled by StringTie, not to the ones in the reference, i.e. the ones in the file, provided with the -G parameter.