I would like to compare two groups (control,disease) which includes 3 replicates in each group. I followed the nature tuxedo protocol (HISAT,Stringtie and ballgown). In this method, There are ~700 genes showed p value<0.05 but the Q value ranges very high(0.5<Q value>0.9). But when i used Tophat-cufflink-cuffdiff protocol, this method gave me reasonable q value<0.05. Why there is a higher Q value in ball gown? All these genes are false positive?. Please help me.