Hi all, I received my sequenced transcriptome and genomic data from my service provider and started working with it. Both the DNA and RNA data passed quality metrics post trimming. But the mapping percentage comes out to be 90% using bowtie-DNA and 85% using Hisat2-RNA. I tried both hg38 and hg19 reference genomes, still the same issue persists. Ill attach the QC metrics here. Kindly let me know where i am making an error. Its paired end data 150bp.