i want to use Htseq-count to be used to count the number of reads for the features i have. i have run the program and got the following as part of my result.
ENSG00000202526 0 ENSG00000206882 0 ENSG00000207129 0 ENSG00000207186 0 ENSG00000207277 0 ENSG00000207341 0 ENSG00000210082 5001 ENSG00000211459 1006 ENSG00000212138 0 ENSG00000212154 0 ENSG00000212171 0 ENSG00000212176 0 ENSG00000212204 0 ENSG00000212237 0
i got up to 500 genes but only about 4 or 5 has counts greater than one. is this correct or have i done something wrongly. thanks so much for your assistance