Hi, I got the output from HT-seq as the following
__no_feature 3138617 2814862 3510969 3772998
__ambiguous 965037 905683 1065946 768189
__too_low_aQual 474675 425696 548364 330561
__not_aligned 300633 246494 331364 211173
__alignment_not_unique 1228830 1114723 1379571 1104518
Is it acceptable to have no feature read 3-4millions while the overall alignment read is around 20-25 millions read ( 98% overall alignment rate using HISAT2)?