RNA_Seq data aligned used uniquely or multi mapped reads impact on result interpretation
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
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You could use a third option.
bbmap.shallows you to use arandomlocation among all possible alignments for a multi-mapping read so you count it one once.