Count files using htseq-count? 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&gt;output.count


What is wrong here ? Are there any alternatives to htseq-count?
I m not sure about htseq-counts but I would suggest go for featureCounts, I will update my answer and share the script/command. Give it a try 

the command i use 

featureCounts -T 50 -C -p -t exon -g gene_id -a /run/media/data2/gencode.v21.annotation.gtf  -o PRIMARY_CELL.txt $(ls *.bam | sort )