strand-specific metagene analysis

Question

[yuabrahamliu]

Hi all, I want to ask for some help on strand-specific RNA-seq metagene construction. I have aligned some adapter-based strand-specific RNA-seq to mm10 genome using STAR and then I want to construct a metagene plot on some group of genes using HTSeq, but I found that for many specfic gene region, both the sense and antisense strand had a large amount of reads. Maybe it is because some are the reads derived from the true RNA sequences, and others are the artificial complementary sequences. But I don't know how can I distinguish them using HTSeq and find the true RNA sequences, then count them to the sense and anti-sense strands to generate the metagene plot. Any suggestion would be appreciated. Thank you so much.