RNASeq PE illumina data - Poor Reverse read quality?

[ellango85]

While trimming the adaptor and low quality RNA-Seq illumina paired end reads in Trimmomatic, I have got more Forward only survive of about 40 to 50%. This study is for estimate the transcript abundance (DEG) at various condition. How is the possibility to continue further...

1. USE singleton reads (R1-For only)
   or
2. Only use both paired (survive) high quality reads (50% of the reads)

Any suggestion, Thanks in Advance

by, Ellango R.