I assembled all reads from all my samples in a single metatranscriptome, used FragGeneScan to predict ORFs and annotated the ORFs using Diamond. Also, I mapped the reads of each sample to the assembled metatranscriptome and got a count table. Then, I created one version of the metatranscriptome fasta file and one version of the Diamond tab file for each sample. They just differ in the parameter magnitude=x.

My question is:

When one of my samples does not have reads mapped to a ORF, do I just use magnitude=0, or I have to remove these ORFs from the fasta file and the diamond file of that sample?

Thank you very much!