Should we keep only the uniquely mapped reads for gene expression

1

Hello,

I am doing the alignment of my RNA-seq paired-end reads with

a.HISAT2 --> stringtie --> DEseq2 
b.STAR --> salmon --> DEseq2

Is it necessary to keep only the uniquely mapped reads before doing gene count?

samtools view -b -q 40 -o output.bam alignments.bam


RNA-seq

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