Hi friends

I have 3 RNA-Seq paired end samples which I want to generate differentially expressed gene list, I used these commands:

samtools sort -n accepted_hits.bam accepted_hits_bam_sorted
samtools view -h accepted_hits_bam_sorted.bam >accepted_hits_sorted.sam

But I'm not sure about the following line that must create count table for DESeq input, is it fine (for paired-end)?

htseq-counts --stranded=no --mode=intersection-nonempty -t exon -i gene_id my.sort.sam annotation.gtf > output.txt

Thanks