Hello, For analysis of the data by rna-sequencing I selected HISAT2 and HTSeq-count for mapping and counting the genes levels, the libraryLayout is paired, I am using the below command for both but the results are not exact as of the original data, because I want to recreate the data. could anyone please tell me what is my mistake? because I checked my commands many times and looked for many tutorials and manuals but I found not any differences.

hisat2 -x /work11/maryam/work13/indexmm10/index -1 SRR00000_1.fastq -2 SRR0000_2.fastq -S SRR00000.sam
htseq-count -s no SRR000000.sam  /work11/maryam/work13/indexmm10/mm10.ensGene.gtf > SRR00000.count

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )