Hi, I prepared a .sam file for a paired-end sample through Hisat2 aligner. Now, I want to create a count file. So, I installed the HTSeq application. The target GTF file(hg19.ensGene.gtf.gz) was downloaded from this link.

Now, I run the below command but in SRR6672521.count I can’t find any information. In fact, htseq-count function does work but the final result file(SRR6672521.count) is empty.

htseq-count -i gene_name SRR6672521.sam  hg19.ncbiRefSeq.gtf  > SRR6672521.count 

I appreciate it if anybody shares his/her comment with me.

Best regards