I have some paired end RNA -seq reads without reference genome. I assembled them by using trinity. because my reads containing specific Lexogen primers, I have been recommended to use bbmap instead of Tophat2 in order to avoid map rate decrease. I assembled the reads with trinity and at the moment I have trinity.fasta file. For the next step that I need to map reads to the transcriptome and calculate the read count, how can I use bbmap? regarding the existing of lexogen primers in the reads that may reduce the map rate, what is the command of bbmap for mapping paired end reads to trinity.fasta file? and what is the command for calculating reads? Please guide me.