I have filtered my illumina pair-end reads (Forward lib-24 million reads, Reverse Lib 24 million) using FASTX_Quality_Filter by applying the Q20 score to 90 percent of bases. (75 bp reads, insert size 200 bp)
But after filtering, I am observing around 18 million reads in a forward library and 20 million reads in a reverse library. I can see here 2 million bases difference between two libraries. Can I use above libraries for making transcriptome assembly purpose given that the number of reads are unequal?