RNA_Seq data aligned used uniquely or multi mapped reads impact on result interpretation

Question

[Diango]

I have some transcriptomic (Whole) sequencing data that I should analyse. I would like to do raw data alignment to a reference genome taking into account the multi mapped reads and uniquely mapped reads. So my questions are :

1- Considering unique and multi-aligned reads, wouldn't this be a source of bias in my results interpretation?

2- By hiding the multi-mapped reads, could I lose information on the expression of important genes?

thank you in advance

[GenoMax]

You could use a third option. bbmap.sh allows you to use a random location among all possible alignments for a multi-mapping read so you count it one once.