RNAseq only paired ends reads using featurecounts, should I pay attention to count only reads match to one strand?

Question

[wang-yanfang]

Dear all,

I have paired ends RNA seq, after clean the reads I only kept paired reads. so after mapping the paired reads to its genome, I used featurecounts to get the reads count of each gene. But I am not sure, should I be careful only count reads matching to one strand?

Thanks for any help and advice.