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. I would like to know the consequences on my transcriptomic analysis results : 1. if I should only focus on uniqueMapping reads (mapped to one loci) and neglect MultiMapping read (mapped to several loci or variants)! 2. or take them all together
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