I am trying to remove adapters from my RNA-seq files obtained from Illumina. I used NEBNext ultra directional kit for illumina for library prep and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) for adaptors and primers. I want to use trimmomatic, it has adapter files for Truseq already, I wonder if anyone used trimmomatic for cleaning adapters from NEBnext instead? What would be the options? Do I need to write a new fasta file for adapters?