ht-seq question

[zjrouc]

Hi, all,

i just got a result from ht-seq. It showed that my interesting gene has 7 counts in the alignment. However, from the view of IGV, i could easily identify much more counts than 7 on this gene. My alignment is from STAR, and i used more stringent parameters to control the multiple alignment, which means there should not be any multiple aligned reads in the output. I am really confused about this.

Any suggestion?