I have a single-ended RNA-seq dataset. I have aligned the dataset to hisat2 snp and tran index for gh38 using the following code:

hisat2 --novel-splicesite-outfile SRR11594433_splicesite.txt --novel-splicesite-infile SRR11594433_splicesite.txt --time --un SRR11594433_unpair.fastq --summary-file SRR11594433_summary.txt --met-file SRR11594433_met.txt --no-unal -x <path to hisat2 transcriptomic index> -U SRR11594433.fastq -S SRR11594433.sam

The output shows that only 15% of the reads are aligned to the transcriptome by hisat2 about which I'm very concerned.

Please let me know what can be the reasons for such low portion of aligned reads and how I can solve this problem.

As indicated in the code, the dataset that I'm analyzing is SRR11594433.fastq. I hope that this can be helpful.