mop_mod - Epinano in transcriptome wide samples

[ADelgadoT]

When we run epinano, we divide the total number of sequences in the reference into several groups and then we subset the initial bam file. I've encountered that when using a transcriptome reference, it is possible that no reads are mapped to the subset of references and thus, epinano fails as the input is empty. How can we avoid this?

Thanks a lot!