I am doing RNA-Seq data analysis using data available on SRA (SRR6047326). Samples are from the pig and they are paired. So, I did alignment using HISAT2.I used pig reference genome available on ENSEMBL. Then, I sorted .sam output files obtained from HISAT2. Now I am trying to get the count file using sorted sam file and it is not working. I am using annotated GTF file for pig which I downloaded from Ensembl.
I get count files using following commands, but all the counts are 0.
htseq-counts -i no myfile.sam genes.gtf>output.count
What is wrong here ? Are there any alternatives to htseq-count?