Im usnig Htseq for counting and the feature type is set to exonic by default so I am assuming that Im getting only exonic reads. How to set the feature type so i get exonic and intronic reads?
I have tried to put on the featue : "-type" but i got higher number of no feature counts
So with default parameter set to exon this is what i get _no_feature 5821188 __ambiguous 419467 __too_low_aQual 0 __not_aligned 0 __alignment_not_unique 14069035
when i write : -type on the parameter i get this no_feature 11616316 __ambiguous 0 __too_low_aQual 0 __not_aligned 0 __alignment_not_unique 14069035
the number of no feature has increased, im not sure how to interpret that
I would like to be sure while using htseq that im couning for both exon and intron