Use normalised reads for HISAT2/Braker1

Question

[ersgupta]

I want to use braker for gene prediction of a denovo genome assembly using RNAseq data. I have 21 RNAseq samples.

My question is, for aligning using HISAT2, is it ok to use the normalised reads (using trinity: coverage 50) or use all 21 RNAseq files separately?

Any suggestion would be appreciated. Thanks