I'm stuck on this question. I have read that I should disable the spliced alignment for Hisat2 when aligning DNA reads, but confused on the results.

So I have my illumina shotgun reads, adapters removed and host removed. I first map with Bowtie2 with Very Sensitive end to end against a reference, which leaves me mapped and unmapped. Then I map the reads again using Hisat2, as it tends to find reads that Bowtie2 misses for some reason. So since what I have read, that I should disable the spliced alignment with Hisat2 when mapping DNA reads, so I did this which again gave me mapped and unmapped reads. Then as a test on the unmapped reads I ran Hisat2 again without disabling the spliced reads option, which again gave me a good number of mapped reads. I took a handfull of the mapped reads, both forward and reverse and ran them on the Online NCBI Blast and it looked like those reads should have been mapped by either Bowtie2 or Hisat2 in the first run. I did not look at the insert size on the reads, so it could have a much larger insert size.

What is the recommendation here??? Should I not disable the spliced alignment or not??