HISAT and HISAT2 errors about hisat2

[infphilo]

HISAT and HISAT2 don't support the --local option and options such as -D, -R, -N, -L, and -i. Would it be possible for you to prepare a small set of reads that I can use to reproduce and fix this runtime error in HISAT2?

[SusieX]

Hi,
I used HISAT2 to align human RNA-seq data (Illumina PE, Stranded, rRNA depleted).
We are interested in comparing gene expression levels, snp and different isoform usage between treatment conditions in the end.
I got about 70-75% reads aligned concordantly 1 time and about 20% concordantly >1 time with less than 10% disconcordantly aligned. Overall mapped rate is over 95%.
Is there a common benchmark that how much % unique concordantly mapped reads is typical for human RNA?
Is human grch38_snp_tran index the right one to use for me? Should I expect difference between using grch38_tran and grch38_snp_tran?
I'm wondering how to determine whether alignment result is acceptable for carrying on the downstream analysis and how I could tweak with the parameters in HISAT if needed.

Thanks,