I am running HT seq using my sam files (obtained from bowtie) and the gtf file I obtained from Ensemble for Phytophthora infestans. Everything is ok except that I am obtaining zero counts on my HTseq output. I have read in other post that it may be because my gtf file uses different identifiers than my sam output. But I really don't know how to fix it and it is somehow urgent! I am analyzing small RNAseq data in four different samples so I need the table counts in order to see if small RNAs are differently expressed.
I will remain attentive!!!