ht seq counting/ Most of reads into alignment non unique

[mirjamp]

Hi all,

I am new to Rna seq. I am runnign ht seq within galaxy but at the end most of my reads end up in alignment non unique

so the parameter im using for ht seq are
mode : union
strandness: reverse
feature type : gene
Im using a gff file from gencode (human)

_no_feature 1029187
__ambiguous 998628
__too_low_aQual 0
__not_aligned 0
__alignment_not_unique 13419757


I have single end read , 75 bp

I am trying to understand why most of the reads are in alignment non unique. Also im not sure if featrure type set to gene would give exoninc and intronic reads as im interested in both.

thank you in advance

Best,
Mirjam