I have paired fastq rna sequences. I am using hisat2 in order to align the reads to my reference based on the following command:
hisat2 --no-spliced-alignment --no-unal -p 2 -x ./reference.fasta -1 ./Data/D10_R1.fastq.gz -2 ./Data/D10_R2.fastq.gz -S D10.sam
Though I am not sure should I keep --no-spliced-alignment tag or not. For RNA data should I consider splices?