Problem to create count file through HTSeq application

Question

[modarzi]

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

[barslmn]

Is there anything on stderr?

There is a similar issue on their GitHub: https://github.com/simon-anders/htseq/issues/97

Try updating to the latest version, sorting your input file by name and converting to bam.

[modarzi]

Hi, Thank you for your comment. I updated to the last version and the problem was solved.

Best wishes