Hi,

I haven't looked into it in much detail so I'm not sure if I'm missing a reason of why it would be intended.
However, when you specify --counts_format linear, for the gene and transcript level counts, only the linear format is saved, while for the transcript model, both the linear and wide format are saved, resulting in increased storage requirements (which are very high in my case).

Many thanks again for the great tool!

Cheers,
Luuk