A question about alignment

[QianhuiWan]

Hello, I have tried this pipeline and found an issue with alignment; most of the reads were not aligned. Is it possible to get the HISAT2 CHM13v2 index files? Thank you so much.

Below is the code I used for generating the CHM13v2 index:
/home/qwan/miniconda3/envs/coh/bin/hisat2-build -p 4 GCA_009914755.4.fa ~/hg38_p14/HISAT2_hg38_CHM13v2/genome

Best regards
Qianhui

[QianhuiWan]

Sorry, I have the Storm-seq data from mice, I have changed the reference genome to mm39, but find the alignment rate is still low for many samples, do you know how to deal with this issue properly, thanks!
This is the parameters I set for HISAT2: --dta --rna-strandness RF -k 1 --known-splicesite-infile /net/nfs-irwrsrchnas01/labs/dschones/bioresearch/qianhui/mm39/HISAT2/splice_sites.txt

Thanks and best regards
Qianhui